-
compute smd/hourglass_error command — LAMMPS documentation
+ compute smd/hourglass/error command — LAMMPS documentation
@@ -109,7 +109,7 @@
compute smd/contact_radius command¶
+compute smd/contact/radius command¶
Syntax¶
-compute ID group-ID smd/contact_radius
+compute ID group-ID smd/contact/radius
- ID, group-ID are documented in compute command -
- smd/contact_radius = style name of this compute command +
- smd/contact/radius = style name of this compute command
Examples¶
-compute 1 all smd/contact_radius
+compute 1 all smd/contact/radius
Description¶
-Define a computation which outputs the contact radius, i.e., the radius used to prevent particles from penetrating each other. -The contact radius is used only to prevent particles belonging to different physical bodies from penetrating each other. It is used by the contact pair styles, -e.g., smd/hertz and smd/tri_surface.
-See this PDF guide to using Smooth Mach Dynamics in -LAMMPS.
+Define a computation which outputs the contact radius, i.e., the +radius used to prevent particles from penetrating each other. The +contact radius is used only to prevent particles belonging to +different physical bodies from penetrating each other. It is used by +the contact pair styles, e.g., smd/hertz and smd/tri_surface.
+See this PDF guide to using Smooth +Mach Dynamics in LAMMPS.
The value of the contact radius will be 0.0 for particles not in the specified compute group.
Output info:
diff --git a/doc/compute_smd_contact_radius.txt b/doc/compute_smd_contact_radius.txt index fea13fcfc3..914357ed76 100644 --- a/doc/compute_smd_contact_radius.txt +++ b/doc/compute_smd_contact_radius.txt @@ -6,27 +6,29 @@ :line -compute smd/contact_radius command :h3 +compute smd/contact/radius command :h3 [Syntax:] -compute ID group-ID smd/contact_radius :pre +compute ID group-ID smd/contact/radius :pre ID, group-ID are documented in "compute"_compute.html command -smd/contact_radius = style name of this compute command :ul +smd/contact/radius = style name of this compute command :ul [Examples:] -compute 1 all smd/contact_radius :pre +compute 1 all smd/contact/radius :pre [Description:] -Define a computation which outputs the contact radius, i.e., the radius used to prevent particles from penetrating each other. -The contact radius is used only to prevent particles belonging to different physical bodies from penetrating each other. It is used by the contact pair styles, -e.g., smd/hertz and smd/tri_surface. +Define a computation which outputs the contact radius, i.e., the +radius used to prevent particles from penetrating each other. The +contact radius is used only to prevent particles belonging to +different physical bodies from penetrating each other. It is used by +the contact pair styles, e.g., smd/hertz and smd/tri_surface. -See "this PDF guide"_USER/smd/SMD_LAMMPS_userguide.pdf to using Smooth Mach Dynamics in -LAMMPS. +See "this PDF guide"_USER/smd/SMD_LAMMPS_userguide.pdf to using Smooth +Mach Dynamics in LAMMPS. The value of the contact radius will be 0.0 for particles not in the specified compute group. diff --git a/doc/compute_smd_hourglass_error.html b/doc/compute_smd_hourglass_error.html index af567fca0e..0bb0e395ab 100644 --- a/doc/compute_smd_hourglass_error.html +++ b/doc/compute_smd_hourglass_error.html @@ -8,7 +8,7 @@ -- Docs » -
- compute smd/hourglass_error command +
- compute smd/hourglass/error command
-
@@ -125,20 +125,20 @@
-
compute smd/hourglass_error command¶
+compute smd/hourglass/error command¶
Syntax¶
-compute ID group-ID smd/hourglass_error +
compute ID group-ID smd/hourglass/error
- ID, group-ID are documented in compute command -
- smd/hourglass_error = style name of this compute command +
- smd/hourglass/error = style name of this compute command
Examples¶
-@@ -148,24 +148,28 @@ relative separation with respect to the actual relative separation of the particles i and j. Ideally, if the deformation gradient is exact, and there exists a unique mapping between all particles’ positions -within the neighborhood of the central node and the deformation gradient, -the approximated relative separation will coincide with the actual relative -separation of the particles i and j in the deformed configuration. -This compute is only really useful for debugging the hourglass control mechanim which is part of the Total-Lagrangian SPH pair style. -compute 1 all smd/hourglass_error +
compute 1 all smd/hourglass/error
See this PDF guide to use Smooth Mach Dynamics in LAMMPS.
+within the neighborhood of the central node and the deformation +gradient, the approximated relative separation will coincide with the +actual relative separation of the particles i and j in the deformed +configuration. This compute is only really useful for debugging the +hourglass control mechanim which is part of the Total-Lagrangian SPH +pair style. +See this PDF guide to use Smooth +Mach Dynamics in LAMMPS.
Output Info:
This compute calculates a per-particle vector, which can be accessed by any command that uses per-particle values from a compute as input. See How-to discussions, section 6.15 for an overview of LAMMPS output options.
-The per-particle vector values will are dimensionless. See units.
+The per-particle vector values will are dimensionless. See +units.
diff --git a/doc/compute_smd_hourglass_error.txt b/doc/compute_smd_hourglass_error.txt index ba87db467a..36978cc9ef 100644 --- a/doc/compute_smd_hourglass_error.txt +++ b/doc/compute_smd_hourglass_error.txt @@ -6,18 +6,18 @@ :line -compute smd/hourglass_error command :h3 +compute smd/hourglass/error command :h3 [Syntax:] -compute ID group-ID smd/hourglass_error :pre +compute ID group-ID smd/hourglass/error :pre ID, group-ID are documented in "compute"_compute.html command -smd/hourglass_error = style name of this compute command :ul +smd/hourglass/error = style name of this compute command :ul [Examples:] -compute 1 all smd/hourglass_error :pre +compute 1 all smd/hourglass/error :pre [Description:] @@ -25,12 +25,15 @@ Define a computation which outputs the error of the approximated relative separation with respect to the actual relative separation of the particles i and j. Ideally, if the deformation gradient is exact, and there exists a unique mapping between all particles' positions -within the neighborhood of the central node and the deformation gradient, -the approximated relative separation will coincide with the actual relative -separation of the particles i and j in the deformed configuration. -This compute is only really useful for debugging the hourglass control mechanim which is part of the Total-Lagrangian SPH pair style. +within the neighborhood of the central node and the deformation +gradient, the approximated relative separation will coincide with the +actual relative separation of the particles i and j in the deformed +configuration. This compute is only really useful for debugging the +hourglass control mechanim which is part of the Total-Lagrangian SPH +pair style. -See "this PDF guide"_USER/smd/SMD_LAMMPS_userguide.pdf to use Smooth Mach Dynamics in LAMMPS. +See "this PDF guide"_USER/smd/SMD_LAMMPS_userguide.pdf to use Smooth +Mach Dynamics in LAMMPS. [Output Info:] @@ -39,15 +42,17 @@ any command that uses per-particle values from a compute as input. See "How-to discussions, section 6.15"_Section_howto.html#howto_15 for an overview of LAMMPS output options. -The per-particle vector values will are dimensionless. See "units"_units.html. +The per-particle vector values will are dimensionless. See +"units"_units.html. [Restrictions:] This compute is part of the USER-SMD package. It is only enabled if -LAMMPS was built with that package. See the "Making LAMMPS"_Section_start.html#start_3 -section for more info. +LAMMPS was built with that package. See the "Making +LAMMPS"_Section_start.html#start_3 section for more info. -This quantity will be computed only for particles which interact with tlsph pair style. +This quantity will be computed only for particles which interact with +tlsph pair style. [Related Commands:] diff --git a/doc/compute_smd_internal_energy.html b/doc/compute_smd_internal_energy.html index 89e92afdd5..e9c6224587 100644 --- a/doc/compute_smd_internal_energy.html +++ b/doc/compute_smd_internal_energy.html @@ -8,7 +8,7 @@ -Restrictions¶
This compute is part of the USER-SMD package. It is only enabled if -LAMMPS was built with that package. See the Making LAMMPS -section for more info.
-This quantity will be computed only for particles which interact with tlsph pair style.
+LAMMPS was built with that package. See the Making LAMMPS section for more info. +This quantity will be computed only for particles which interact with +tlsph pair style.
Related Commands:
compute smd/internal_energy command — LAMMPS documentation +compute smd/internal/energy command — LAMMPS documentation @@ -109,7 +109,7 @@- Docs » -
- compute smd/internal_energy command +
- compute smd/internal/energy command
-
@@ -125,40 +125,42 @@
-
compute smd/internal_energy command¶
+compute smd/internal/energy command¶
Syntax¶
-compute ID group-ID smd/internal_energy +
compute ID group-ID smd/internal/energy
- ID, group-ID are documented in compute command -
- smd/smd/internal_energy = style name of this compute command +
- smd/smd/internal/energy = style name of this compute command
Examples¶
-compute 1 all smd/internal_energy +
compute 1 all smd/internal/energy
Description¶
-Define a computation which outputs the per-particle enthalpy, i.e., the sum of potential energy and heat.
-See this PDF guide to use Smooth Mach Dynamics in LAMMPS.
+Define a computation which outputs the per-particle enthalpy, i.e., +the sum of potential energy and heat.
+See this PDF guide to use Smooth +Mach Dynamics in LAMMPS.
Output Info:
-This compute calculates a per-particle vector, which can be accessed by -any command that uses per-particle values from a compute as input. See -How-to discussions, section 6.15 -for an overview of LAMMPS output options.
+This compute calculates a per-particle vector, which can be accessed +by any command that uses per-particle values from a compute as input. +See How-to discussions, section 6.15 for +an overview of LAMMPS output options.
The per-particle vector values will be given in units of energy.
Restrictions¶
This compute is part of the USER-SMD package. It is only enabled if -LAMMPS was built with that package. See the Making LAMMPS -section for more info. This compute can only be used for particles which interact via the -updated Lagrangian or total Lagrangian SPH pair styles.
+LAMMPS was built with that package. See the Making LAMMPS section for more info. This compute +can only be used for particles which interact via the updated +Lagrangian or total Lagrangian SPH pair styles.Related Commands:
diff --git a/doc/compute_smd_internal_energy.txt b/doc/compute_smd_internal_energy.txt index d52a3936ad..f556b79c3e 100644 --- a/doc/compute_smd_internal_energy.txt +++ b/doc/compute_smd_internal_energy.txt @@ -6,44 +6,44 @@ :line -compute smd/internal_energy command :h3 +compute smd/internal/energy command :h3 [Syntax:] -compute ID group-ID smd/internal_energy :pre +compute ID group-ID smd/internal/energy :pre ID, group-ID are documented in "compute"_compute.html command -smd/smd/internal_energy = style name of this compute command :ul +smd/smd/internal/energy = style name of this compute command :ul [Examples:] -compute 1 all smd/internal_energy :pre +compute 1 all smd/internal/energy :pre [Description:] -Define a computation which outputs the per-particle enthalpy, i.e., the sum of potential energy and heat. +Define a computation which outputs the per-particle enthalpy, i.e., +the sum of potential energy and heat. -See "this PDF guide"_USER/smd/SMD_LAMMPS_userguide.pdf to use Smooth Mach Dynamics in LAMMPS. +See "this PDF guide"_USER/smd/SMD_LAMMPS_userguide.pdf to use Smooth +Mach Dynamics in LAMMPS. [Output Info:] -This compute calculates a per-particle vector, which can be accessed by -any command that uses per-particle values from a compute as input. See -"How-to discussions, section 6.15"_Section_howto.html#howto_15 -for an overview of LAMMPS output options. +This compute calculates a per-particle vector, which can be accessed +by any command that uses per-particle values from a compute as input. +See "How-to discussions, section 6.15"_Section_howto.html#howto_15 for +an overview of LAMMPS output options. The per-particle vector values will be given in "units"_units.html of energy. [Restrictions:] This compute is part of the USER-SMD package. It is only enabled if -LAMMPS was built with that package. See the "Making LAMMPS"_Section_start.html#start_3 -section for more info. This compute can only be used for particles which interact via the -updated Lagrangian or total Lagrangian SPH pair styles. - +LAMMPS was built with that package. See the "Making +LAMMPS"_Section_start.html#start_3 section for more info. This compute +can only be used for particles which interact via the updated +Lagrangian or total Lagrangian SPH pair styles. [Related Commands:] - - [Default:] diff --git a/doc/compute_smd_plastic_strain.html b/doc/compute_smd_plastic_strain.html index 25d27a9d3e..aed081f816 100644 --- a/doc/compute_smd_plastic_strain.html +++ b/doc/compute_smd_plastic_strain.html @@ -8,7 +8,7 @@ -compute smd/plastic_strain command — LAMMPS documentation +compute smd/plastic/strain command — LAMMPS documentation @@ -109,7 +109,7 @@- Docs » -
- compute smd/plastic_strain command +
- compute smd/plastic/strain command
-
@@ -125,46 +125,49 @@
-
compute smd/plastic_strain command¶
+compute smd/plastic/strain command¶
Syntax¶
-compute ID group-ID smd/plastic_strain +
compute ID group-ID smd/plastic/strain
- ID, group-ID are documented in compute command -
- smd/plastic_strain = style name of this compute command +
- smd/plastic/strain = style name of this compute command
Examples¶
-diff --git a/doc/compute_smd_plastic_strain.txt b/doc/compute_smd_plastic_strain.txt index 0951677ee8..c149bc96c7 100644 --- a/doc/compute_smd_plastic_strain.txt +++ b/doc/compute_smd_plastic_strain.txt @@ -6,46 +6,49 @@ :line -compute smd/plastic_strain command :h3 +compute smd/plastic/strain command :h3 [Syntax:] -compute ID group-ID smd/plastic_strain :pre +compute ID group-ID smd/plastic/strain :pre ID, group-ID are documented in "compute"_compute.html command -smd/plastic_strain = style name of this compute command :ul +smd/plastic/strain = style name of this compute command :ul [Examples:] -compute 1 all smd/plastic_strain :pre +compute 1 all smd/plastic/strain :pre [Description:] -Define a computation that outputs the equivalent plastic strain per particle. -This command is only meaningful if a material model with plasticity is defined. +Define a computation that outputs the equivalent plastic strain per +particle. This command is only meaningful if a material model with +plasticity is defined. - -See "this PDF guide"_USER/smd/SMD_LAMMPS_userguide.pdf to use Smooth Mach Dynamics in LAMMPS. +See "this PDF guide"_USER/smd/SMD_LAMMPS_userguide.pdf to use Smooth +Mach Dynamics in LAMMPS. [Output Info:] -This compute calculates a per-particle vector, which can be accessed by -any command that uses per-particle values from a compute as input. See -"How-to discussions, section 6.15"_Section_howto.html#howto_15 -for an overview of LAMMPS output options. +This compute calculates a per-particle vector, which can be accessed +by any command that uses per-particle values from a compute as input. +See "How-to discussions, section 6.15"_Section_howto.html#howto_15 for +an overview of LAMMPS output options. The per-particle values will be given dimensionless. See "units"_units.html. [Restrictions:] This compute is part of the USER-SMD package. It is only enabled if -LAMMPS was built with that package. See the "Making LAMMPS"_Section_start.html#start_3 -section for more info. This compute can only be used for particles which interact via the -updated Lagrangian or total Lagrangian SPH pair styles. +LAMMPS was built with that package. See the "Making +LAMMPS"_Section_start.html#start_3 section for more info. This compute +can only be used for particles which interact via the updated +Lagrangian or total Lagrangian SPH pair styles. [Related commands:] -"smd/plastic_strain_rate"_compute_smd_tlsph_strain.html, "smd/tlsph_strain_rate"_compute_smd_tlsph_strain_rate.html, -"smd/tlsph_strain"_compute_smd_tlsph_strain.html +"smd/plastic/strain/rate"_compute_smd_tlsph_strain.html, +"smd/tlsph/strain/rate"_compute_smd_tlsph_strain_rate.html, +"smd/tlsph/strain"_compute_smd_tlsph_strain.html -[Default:] none \ No newline at end of file +[Default:] none diff --git a/doc/compute_smd_plastic_strain_rate.html b/doc/compute_smd_plastic_strain_rate.html index 40c21935dd..8ffcfd4f4d 100644 --- a/doc/compute_smd_plastic_strain_rate.html +++ b/doc/compute_smd_plastic_strain_rate.html @@ -8,7 +8,7 @@ -compute 1 all smd/plastic_strain +
compute 1 all smd/plastic/strain
Description¶
-Define a computation that outputs the equivalent plastic strain per particle. -This command is only meaningful if a material model with plasticity is defined.
-See this PDF guide to use Smooth Mach Dynamics in LAMMPS.
+Define a computation that outputs the equivalent plastic strain per +particle. This command is only meaningful if a material model with +plasticity is defined.
+See this PDF guide to use Smooth +Mach Dynamics in LAMMPS.
Output Info:
-This compute calculates a per-particle vector, which can be accessed by -any command that uses per-particle values from a compute as input. See -How-to discussions, section 6.15 -for an overview of LAMMPS output options.
+This compute calculates a per-particle vector, which can be accessed +by any command that uses per-particle values from a compute as input. +See How-to discussions, section 6.15 for +an overview of LAMMPS output options.
The per-particle values will be given dimensionless. See units.
Restrictions¶
This compute is part of the USER-SMD package. It is only enabled if -LAMMPS was built with that package. See the Making LAMMPS -section for more info. This compute can only be used for particles which interact via the -updated Lagrangian or total Lagrangian SPH pair styles.
+LAMMPS was built with that package. See the Making LAMMPS section for more info. This compute +can only be used for particles which interact via the updated +Lagrangian or total Lagrangian SPH pair styles.Related commands¶
-smd/plastic_strain_rate, smd/tlsph_strain_rate, -smd/tlsph_strain
+smd/plastic/strain/rate, +smd/tlsph/strain/rate, +smd/tlsph/strain
Default: none
compute smd/plastic_strain_rate command — LAMMPS documentation +compute smd/plastic/strain/rate command — LAMMPS documentation @@ -109,7 +109,7 @@- Docs » -
- compute smd/plastic_strain_rate command +
- compute smd/plastic/strain/rate command
-
@@ -125,46 +125,49 @@
-
compute smd/plastic_strain_rate command¶
+compute smd/plastic/strain/rate command¶
Syntax¶
-diff --git a/doc/compute_smd_rho.txt b/doc/compute_smd_rho.txt index 3ae8c7e7a6..1d4ca6329f 100644 --- a/doc/compute_smd_rho.txt +++ b/doc/compute_smd_rho.txt @@ -23,27 +23,29 @@ compute 1 all smd/rho :pre Define a computation that calculates the per-particle mass density. The mass density is the mass of a particle which is constant during -the course of a simulation, divided by its volume, which can change due to mechanical deformation. +the course of a simulation, divided by its volume, which can change +due to mechanical deformation. -See "this PDF guide"_USER/smd/SMD_LAMMPS_userguide.pdf to use Smooth Mach Dynamics in LAMMPS. +See "this PDF guide"_USER/smd/SMD_LAMMPS_userguide.pdf to use Smooth +Mach Dynamics in LAMMPS. [Output info:] -This compute calculates a per-particle vector, which can be accessed by -any command that uses per-particle values from a compute as input. See -"How-to discussions, section 6.15"_Section_howto.html#howto_15 -for an overview of LAMMPS output options. +This compute calculates a per-particle vector, which can be accessed +by any command that uses per-particle values from a compute as input. +See "How-to discussions, section 6.15"_Section_howto.html#howto_15 for +an overview of LAMMPS output options. The per-particle values will be in "units"_units.html of mass over volume. [Restrictions:] This compute is part of the USER-SMD package. It is only enabled if -LAMMPS was built with that package. See the "Making LAMMPS"_Section_start.html#start_3 -section for more info. +LAMMPS was built with that package. See the "Making +LAMMPS"_Section_start.html#start_3 section for more info. [Related commands:] -"smd/vol"_compute_smd_vol.html +"compute smd/vol"_compute_smd_vol.html [Default:] none diff --git a/doc/compute_smd_tlsph_defgrad.html b/doc/compute_smd_tlsph_defgrad.html index 7c83a2d624..0485ddccaa 100644 --- a/doc/compute_smd_tlsph_defgrad.html +++ b/doc/compute_smd_tlsph_defgrad.html @@ -8,7 +8,7 @@ -compute ID group-ID smd/plastic_strain_rate +
compute ID group-ID smd/plastic/strain/rate
- ID, group-ID are documented in compute command -
- smd/plastic_strain_rate = style name of this compute command +
- smd/plastic/strain/rate = style name of this compute command
Examples¶
-diff --git a/doc/compute_smd_plastic_strain_rate.txt b/doc/compute_smd_plastic_strain_rate.txt index 8879a63786..2b222b9a78 100644 --- a/doc/compute_smd_plastic_strain_rate.txt +++ b/doc/compute_smd_plastic_strain_rate.txt @@ -6,45 +6,49 @@ :line -compute smd/plastic_strain_rate command :h3 +compute smd/plastic/strain/rate command :h3 [Syntax:] -compute ID group-ID smd/plastic_strain_rate :pre +compute ID group-ID smd/plastic/strain/rate :pre ID, group-ID are documented in "compute"_compute.html command -smd/plastic_strain_rate = style name of this compute command :ul +smd/plastic/strain/rate = style name of this compute command :ul [Examples:] -compute 1 all smd/plastic_strain_rate :pre +compute 1 all smd/plastic/strain/rate :pre [Description:] -Define a computation that outputs the time rate of the equivalent plastic strain. -This command is only meaningful if a material model with plasticity is defined. +Define a computation that outputs the time rate of the equivalent +plastic strain. This command is only meaningful if a material model +with plasticity is defined. -See "this PDF guide"_USER/smd/SMD_LAMMPS_userguide.pdf to use Smooth Mach Dynamics in LAMMPS. +See "this PDF guide"_USER/smd/SMD_LAMMPS_userguide.pdf to use Smooth +Mach Dynamics in LAMMPS. [Output Info:] -This compute calculates a per-particle vector, which can be accessed by -any command that uses per-particle values from a compute as input. See -"How-to discussions, section 6.15"_Section_howto.html#howto_15 -for an overview of LAMMPS output options. +This compute calculates a per-particle vector, which can be accessed +by any command that uses per-particle values from a compute as input. +See "How-to discussions, section 6.15"_Section_howto.html#howto_15 for +an overview of LAMMPS output options. The per-particle values will be given in "units"_units.html of one over time. [Restrictions:] This compute is part of the USER-SMD package. It is only enabled if -LAMMPS was built with that package. See the "Making LAMMPS"_Section_start.html#start_3 -section for more info. This compute can only be used for particles which interact via the -updated Lagrangian or total Lagrangian SPH pair styles. +LAMMPS was built with that package. See the "Making +LAMMPS"_Section_start.html#start_3 section for more info. This compute +can only be used for particles which interact via the updated +Lagrangian or total Lagrangian SPH pair styles. [Related commands:] -"smd/plastic_strain"_compute_smd_plastic_strain.html, "smd/tlsph_strain_rate"_compute_smd_tlsph_strain_rate.html, -"smd/tlsph_strain"_compute_smd_tlsph_strain.html +"smd/plastic/strain"_compute_smd_plastic_strain.html, +"smd/tlsph/strain/rate"_compute_smd_tlsph_strain_rate.html, +"smd/tlsph/strain"_compute_smd_tlsph_strain.html -[Default:] none \ No newline at end of file +[Default:] none diff --git a/doc/compute_smd_rho.html b/doc/compute_smd_rho.html index b65cc0d866..7ac4630dab 100644 --- a/doc/compute_smd_rho.html +++ b/doc/compute_smd_rho.html @@ -146,24 +146,25 @@compute 1 all smd/plastic_strain_rate +
compute 1 all smd/plastic/strain/rate
Description¶
-Define a computation that outputs the time rate of the equivalent plastic strain. -This command is only meaningful if a material model with plasticity is defined.
-See this PDF guide to use Smooth Mach Dynamics in LAMMPS.
+Define a computation that outputs the time rate of the equivalent +plastic strain. This command is only meaningful if a material model +with plasticity is defined.
+See this PDF guide to use Smooth +Mach Dynamics in LAMMPS.
Output Info:
-This compute calculates a per-particle vector, which can be accessed by -any command that uses per-particle values from a compute as input. See -How-to discussions, section 6.15 -for an overview of LAMMPS output options.
+This compute calculates a per-particle vector, which can be accessed +by any command that uses per-particle values from a compute as input. +See How-to discussions, section 6.15 for +an overview of LAMMPS output options.
The per-particle values will be given in units of one over time.
Restrictions¶
This compute is part of the USER-SMD package. It is only enabled if -LAMMPS was built with that package. See the Making LAMMPS -section for more info. This compute can only be used for particles which interact via the -updated Lagrangian or total Lagrangian SPH pair styles.
+LAMMPS was built with that package. See the Making LAMMPS section for more info. This compute +can only be used for particles which interact via the updated +Lagrangian or total Lagrangian SPH pair styles.Related commands¶
-smd/plastic_strain, smd/tlsph_strain_rate, -smd/tlsph_strain
+smd/plastic/strain, +smd/tlsph/strain/rate, +smd/tlsph/strain
Default: none
Description¶
Define a computation that calculates the per-particle mass density. The mass density is the mass of a particle which is constant during -the course of a simulation, divided by its volume, which can change due to mechanical deformation.
-See this PDF guide to use Smooth Mach Dynamics in LAMMPS.
+the course of a simulation, divided by its volume, which can change +due to mechanical deformation. +See this PDF guide to use Smooth +Mach Dynamics in LAMMPS.
Output info:
-This compute calculates a per-particle vector, which can be accessed by -any command that uses per-particle values from a compute as input. See -How-to discussions, section 6.15 -for an overview of LAMMPS output options.
+This compute calculates a per-particle vector, which can be accessed +by any command that uses per-particle values from a compute as input. +See How-to discussions, section 6.15 for +an overview of LAMMPS output options.
The per-particle values will be in units of mass over volume.
Restrictions¶
This compute is part of the USER-SMD package. It is only enabled if -LAMMPS was built with that package. See the Making LAMMPS -section for more info.
+LAMMPS was built with that package. See the Making LAMMPS section for more info.compute smd/tlsph_defgrad command — LAMMPS documentation +compute smd/tlsph/defgrad command — LAMMPS documentation @@ -109,7 +109,7 @@- Docs » -
- compute smd/tlsph_defgrad command +
- compute smd/tlsph/defgrad command
-
@@ -125,48 +125,51 @@
-
compute smd/tlsph_defgrad command¶
+compute smd/tlsph/defgrad command¶
Syntax¶
-compute ID group-ID smd/tlsph_defgrad +
compute ID group-ID smd/tlsph/defgrad
- ID, group-ID are documented in compute command -
- smd/tlsph_defgrad = style name of this compute command +
- smd/tlsph/defgrad = style name of this compute command
Examples¶
-diff --git a/doc/compute_smd_tlsph_defgrad.txt b/doc/compute_smd_tlsph_defgrad.txt index e7c3514a63..86351e42f7 100644 --- a/doc/compute_smd_tlsph_defgrad.txt +++ b/doc/compute_smd_tlsph_defgrad.txt @@ -6,48 +6,52 @@ :line -compute smd/tlsph_defgrad command :h3 +compute smd/tlsph/defgrad command :h3 [Syntax:] -compute ID group-ID smd/tlsph_defgrad :pre +compute ID group-ID smd/tlsph/defgrad :pre ID, group-ID are documented in "compute"_compute.html command -smd/tlsph_defgrad = style name of this compute command :ul +smd/tlsph/defgrad = style name of this compute command :ul [Examples:] -compute 1 all smd/tlsph_defgrad :pre +compute 1 all smd/tlsph/defgrad :pre [Description:] -Define a computation that calculates the deformation gradient. -It is only meaningful for particles which interact according to the Total-Lagrangian SPH pair style. +Define a computation that calculates the deformation gradient. It is +only meaningful for particles which interact according to the +Total-Lagrangian SPH pair style. -See "this PDF guide"_USER/smd/SMD_LAMMPS_userguide.pdf to use Smooth Mach Dynamics in -LAMMPS. +See "this PDF guide"_USER/smd/SMD_LAMMPS_userguide.pdf to use Smooth +Mach Dynamics in LAMMPS. [Output info:] -This compute outputss a per-particle vector of vectors (tensors), which can be -accessed by any command that uses per-particle values from a compute as input. See -"How-to discussions, section 6.15"_Section_howto.html#howto_15 -for an overview of LAMMPS output options. - -The per-particle vector values will be given dimensionless. See "units"_units.html. -The per-particle vector has 10 entries. The first nine entries correspond to the xx, xy, xz, yx, yy, yz, zx, zy, zz components -of the asymmetric deformation gradient tensor. The tenth entry is the determinant of the deformation gradient. +This compute outputss a per-particle vector of vectors (tensors), +which can be accessed by any command that uses per-particle values +from a compute as input. See "How-to discussions, section +6.15"_Section_howto.html#howto_15 for an overview of LAMMPS output +options. +The per-particle vector values will be given dimensionless. See +"units"_units.html. The per-particle vector has 10 entries. The first +nine entries correspond to the xx, xy, xz, yx, yy, yz, zx, zy, zz +components of the asymmetric deformation gradient tensor. The tenth +entry is the determinant of the deformation gradient. [Restrictions:] -This compute is part of the USER-SMD package. It is only enabled if LAMMPS was -built with that package. See the "Making LAMMPS"_Section_start.html#start_3 -section for more info. TThis compute can only be used for particles which interact via the -total Lagrangian SPH pair style. +This compute is part of the USER-SMD package. It is only enabled if +LAMMPS was built with that package. See the "Making +LAMMPS"_Section_start.html#start_3 section for more info. TThis +compute can only be used for particles which interact via the total +Lagrangian SPH pair style. [Related commands:] -"smd/hourglass_error"_compute_smd_hourglass_error.html +"smd/hourglass/error"_compute_smd_hourglass_error.html [Default:] none diff --git a/doc/compute_smd_tlsph_dt.html b/doc/compute_smd_tlsph_dt.html index 8c97f3839c..a3909df008 100644 --- a/doc/compute_smd_tlsph_dt.html +++ b/doc/compute_smd_tlsph_dt.html @@ -8,7 +8,7 @@ -compute 1 all smd/tlsph_defgrad +
compute 1 all smd/tlsph/defgrad
Description¶
-Define a computation that calculates the deformation gradient. -It is only meaningful for particles which interact according to the Total-Lagrangian SPH pair style.
-See this PDF guide to use Smooth Mach Dynamics in -LAMMPS.
+Define a computation that calculates the deformation gradient. It is +only meaningful for particles which interact according to the +Total-Lagrangian SPH pair style.
+See this PDF guide to use Smooth +Mach Dynamics in LAMMPS.
Output info:
-This compute outputss a per-particle vector of vectors (tensors), which can be -accessed by any command that uses per-particle values from a compute as input. See -How-to discussions, section 6.15 -for an overview of LAMMPS output options.
-The per-particle vector values will be given dimensionless. See units. -The per-particle vector has 10 entries. The first nine entries correspond to the xx, xy, xz, yx, yy, yz, zx, zy, zz components -of the asymmetric deformation gradient tensor. The tenth entry is the determinant of the deformation gradient.
+This compute outputss a per-particle vector of vectors (tensors), +which can be accessed by any command that uses per-particle values +from a compute as input. See How-to discussions, section 6.15 for an overview of LAMMPS output +options.
+The per-particle vector values will be given dimensionless. See +units. The per-particle vector has 10 entries. The first +nine entries correspond to the xx, xy, xz, yx, yy, yz, zx, zy, zz +components of the asymmetric deformation gradient tensor. The tenth +entry is the determinant of the deformation gradient.
Restrictions¶
-This compute is part of the USER-SMD package. It is only enabled if LAMMPS was -built with that package. See the Making LAMMPS -section for more info. TThis compute can only be used for particles which interact via the -total Lagrangian SPH pair style.
+This compute is part of the USER-SMD package. It is only enabled if +LAMMPS was built with that package. See the Making LAMMPS section for more info. TThis +compute can only be used for particles which interact via the total +Lagrangian SPH pair style.
compute smd/tlsph_dt command — LAMMPS documentation +compute smd/tlsph/dt command — LAMMPS documentation @@ -109,7 +109,7 @@- Docs » -
- compute smd/tlsph_dt command +
- compute smd/tlsph/dt command
-
@@ -125,49 +125,52 @@
-
compute smd/tlsph_dt command¶
+compute smd/tlsph/dt command¶
Syntax¶
-compute ID group-ID smd/tlsph_dt +
compute ID group-ID smd/tlsph/dt
- ID, group-ID are documented in compute command -
- smd/tlsph_dt = style name of this compute command +
- smd/tlsph/dt = style name of this compute command
Examples¶
-diff --git a/doc/compute_smd_tlsph_dt.txt b/doc/compute_smd_tlsph_dt.txt index 10cdd1a75a..1f1aa5bcfc 100644 --- a/doc/compute_smd_tlsph_dt.txt +++ b/doc/compute_smd_tlsph_dt.txt @@ -6,49 +6,53 @@ :line -compute smd/tlsph_dt command :h3 +compute smd/tlsph/dt command :h3 [Syntax:] -compute ID group-ID smd/tlsph_dt :pre +compute ID group-ID smd/tlsph/dt :pre ID, group-ID are documented in "compute"_compute.html command -smd/tlsph_dt = style name of this compute command :ul +smd/tlsph/dt = style name of this compute command :ul [Examples:] -compute 1 all smd/tlsph_dt :pre +compute 1 all smd/tlsph/dt :pre [Description:] -Define a computation that outputs the CFL-stable time increment per particle. -This time increment is essentially given by the speed of sound, divided by the SPH smoothing length. -Because both the speed of sound and the smoothing length typically change during the course of a simulation, -the stable time increment needs to be recomputed every time step. -This calculation is performed automatically in the relevant SPH pair styles and this compute only serves to make the -stable time increment accessible for output purposes. +Define a computation that outputs the CFL-stable time increment per +particle. This time increment is essentially given by the speed of +sound, divided by the SPH smoothing length. Because both the speed of +sound and the smoothing length typically change during the course of a +simulation, the stable time increment needs to be recomputed every +time step. This calculation is performed automatically in the +relevant SPH pair styles and this compute only serves to make the +stable time increment accessible for output purposes. -See "this PDF guide"_USER/smd/SMD_LAMMPS_userguide.pdf to using Smooth Mach Dynamics in LAMMPS. +See "this PDF guide"_USER/smd/SMD_LAMMPS_userguide.pdf to using Smooth +Mach Dynamics in LAMMPS. [Output info:] -This compute calculates a per-particle vector, which can be accessed by -any command that uses per-particle values from a compute as input. See -"How-to discussions, section 6.15"_Section_howto.html#howto_15 -for an overview of LAMMPS output options. +This compute calculates a per-particle vector, which can be accessed +by any command that uses per-particle values from a compute as input. +See "How-to discussions, section 6.15"_Section_howto.html#howto_15 for +an overview of LAMMPS output options. The per-particle values will be given in "units"_units.html of time. [Restrictions:] This compute is part of the USER-SMD package. It is only enabled if -LAMMPS was built with that package. See the "Making LAMMPS"_Section_start.html#start_3 -section for more info. +LAMMPS was built with that package. See the "Making +LAMMPS"_Section_start.html#start_3 section for more info. -This compute can only be used for particles interacting with the Total-Lagrangian SPH pair style. +This compute can only be used for particles interacting with the +Total-Lagrangian SPH pair style. [Related commands:] -"smd/adjust_dt"_fix_smd_adjust_dt.html +"smd/adjust/dt"_fix_smd_adjust_dt.html [Default:] none diff --git a/doc/compute_smd_tlsph_num_neighs.html b/doc/compute_smd_tlsph_num_neighs.html index 609e85b380..5caa96ddd9 100644 --- a/doc/compute_smd_tlsph_num_neighs.html +++ b/doc/compute_smd_tlsph_num_neighs.html @@ -8,7 +8,7 @@ -compute 1 all smd/tlsph_dt +
compute 1 all smd/tlsph/dt
Description¶
-Define a computation that outputs the CFL-stable time increment per particle. -This time increment is essentially given by the speed of sound, divided by the SPH smoothing length. -Because both the speed of sound and the smoothing length typically change during the course of a simulation, -the stable time increment needs to be recomputed every time step. -This calculation is performed automatically in the relevant SPH pair styles and this compute only serves to make the +
Define a computation that outputs the CFL-stable time increment per +particle. This time increment is essentially given by the speed of +sound, divided by the SPH smoothing length. Because both the speed of +sound and the smoothing length typically change during the course of a +simulation, the stable time increment needs to be recomputed every +time step. This calculation is performed automatically in the +relevant SPH pair styles and this compute only serves to make the stable time increment accessible for output purposes.
-See this PDF guide to using Smooth Mach Dynamics in LAMMPS.
+See this PDF guide to using Smooth +Mach Dynamics in LAMMPS.
Output info:
-This compute calculates a per-particle vector, which can be accessed by -any command that uses per-particle values from a compute as input. See -How-to discussions, section 6.15 -for an overview of LAMMPS output options.
+This compute calculates a per-particle vector, which can be accessed +by any command that uses per-particle values from a compute as input. +See How-to discussions, section 6.15 for +an overview of LAMMPS output options.
The per-particle values will be given in units of time.
Restrictions¶
This compute is part of the USER-SMD package. It is only enabled if -LAMMPS was built with that package. See the Making LAMMPS -section for more info.
-This compute can only be used for particles interacting with the Total-Lagrangian SPH pair style.
+LAMMPS was built with that package. See the Making LAMMPS section for more info. +This compute can only be used for particles interacting with the +Total-Lagrangian SPH pair style.
compute smd/tlsph_num_neighs command — LAMMPS documentation +compute smd/tlsph/num/neighs command — LAMMPS documentation @@ -109,7 +109,7 @@- Docs » -
- compute smd/tlsph_num_neighs command +
- compute smd/tlsph/num/neighs command
-
@@ -125,45 +125,47 @@
-
compute smd/tlsph_num_neighs command¶
+compute smd/tlsph/num/neighs command¶
Syntax¶
-compute ID group-ID smd/tlsph_num_neighs +
compute ID group-ID smd/tlsph/num/neighs
- ID, group-ID are documented in compute command -
- smd/tlsph_num_neighs = style name of this compute command +
- smd/tlsph/num/neighs = style name of this compute command
Examples¶
-diff --git a/doc/compute_smd_tlsph_num_neighs.txt b/doc/compute_smd_tlsph_num_neighs.txt index b699710597..7c64342012 100644 --- a/doc/compute_smd_tlsph_num_neighs.txt +++ b/doc/compute_smd_tlsph_num_neighs.txt @@ -6,45 +6,48 @@ :line -compute smd/tlsph_num_neighs command :h3 +compute smd/tlsph/num/neighs command :h3 [Syntax:] -compute ID group-ID smd/tlsph_num_neighs :pre +compute ID group-ID smd/tlsph/num/neighs :pre ID, group-ID are documented in "compute"_compute.html command -smd/tlsph_num_neighs = style name of this compute command :ul +smd/tlsph/num/neighs = style name of this compute command :ul [Examples:] -compute 1 all smd/tlsph_num_neighs :pre +compute 1 all smd/tlsph/num/neighs :pre [Description:] -Define a computation that calculates the number of particles -inside of the smoothing kernel radius for particles interacting via the Total-Lagrangian SPH pair style. +Define a computation that calculates the number of particles inside of +the smoothing kernel radius for particles interacting via the +Total-Lagrangian SPH pair style. -See "this PDF guide"_USER/smd/SMD_LAMMPS_userguide.pdf to using Smooth Mach Dynamics in LAMMPS. +See "this PDF guide"_USER/smd/SMD_LAMMPS_userguide.pdf to using Smooth +Mach Dynamics in LAMMPS. [Output info:] -This compute calculates a per-particle vector, which can be accessed by -any command that uses per-particle values from a compute as input. See -"How-to discussions, section 6.15"_Section_howto.html#howto_15 -for an overview of LAMMPS output options. +This compute calculates a per-particle vector, which can be accessed +by any command that uses per-particle values from a compute as input. +See "How-to discussions, section 6.15"_Section_howto.html#howto_15 for +an overview of LAMMPS output options. The per-particle values are dimensionless. See "units"_units.html. [Restrictions:] This compute is part of the USER-SMD package. It is only enabled if -LAMMPS was built with that package. See the "Making LAMMPS"_Section_start.html#start_3 -section for more info. +LAMMPS was built with that package. See the "Making +LAMMPS"_Section_start.html#start_3 section for more info. -This quantity will be computed only for particles which interact with the Total-Lagrangian pair style. +This quantity will be computed only for particles which interact with +the Total-Lagrangian pair style. [Related commands:] -"smd/ulsph_num_neighs"_compute_smd/ulsph_num_neighs.html +"smd/ulsph/num/neighs"_compute_smd_ulsph_num_neighs.html [Default:] none diff --git a/doc/compute_smd_tlsph_shape.html b/doc/compute_smd_tlsph_shape.html index 12f19152f9..72270614e9 100644 --- a/doc/compute_smd_tlsph_shape.html +++ b/doc/compute_smd_tlsph_shape.html @@ -8,7 +8,7 @@ -compute 1 all smd/tlsph_num_neighs +
compute 1 all smd/tlsph/num/neighs
Description¶
-Define a computation that calculates the number of particles -inside of the smoothing kernel radius for particles interacting via the Total-Lagrangian SPH pair style.
-See this PDF guide to using Smooth Mach Dynamics in LAMMPS.
+Define a computation that calculates the number of particles inside of +the smoothing kernel radius for particles interacting via the +Total-Lagrangian SPH pair style.
+See this PDF guide to using Smooth +Mach Dynamics in LAMMPS.
Output info:
-This compute calculates a per-particle vector, which can be accessed by -any command that uses per-particle values from a compute as input. See -How-to discussions, section 6.15 -for an overview of LAMMPS output options.
+This compute calculates a per-particle vector, which can be accessed +by any command that uses per-particle values from a compute as input. +See How-to discussions, section 6.15 for +an overview of LAMMPS output options.
The per-particle values are dimensionless. See units.
Restrictions¶
This compute is part of the USER-SMD package. It is only enabled if -LAMMPS was built with that package. See the Making LAMMPS -section for more info.
-This quantity will be computed only for particles which interact with the Total-Lagrangian pair style.
+LAMMPS was built with that package. See the Making LAMMPS section for more info. +This quantity will be computed only for particles which interact with +the Total-Lagrangian pair style.
compute smd/tlsph_shape command — LAMMPS documentation +compute smd/tlsph/shape command — LAMMPS documentation @@ -109,7 +109,7 @@- Docs » -
- compute smd/tlsph_shape command +
- compute smd/tlsph/shape command
-
@@ -125,47 +125,54 @@
-
compute smd/tlsph_shape command¶
+compute smd/tlsph/shape command¶
Syntax¶
-compute ID group-ID smd/tlsph_shape +
compute ID group-ID smd/tlsph/shape
- ID, group-ID are documented in compute command -
- smd/tlsph_shape = style name of this compute command +
- smd/tlsph/shape = style name of this compute command
Examples¶
-diff --git a/doc/compute_smd_tlsph_shape.txt b/doc/compute_smd_tlsph_shape.txt index a9a69b05e1..d95d95acf1 100644 --- a/doc/compute_smd_tlsph_shape.txt +++ b/doc/compute_smd_tlsph_shape.txt @@ -6,47 +6,56 @@ :line -compute smd/tlsph_shape command :h3 +compute smd/tlsph/shape command :h3 [Syntax:] -compute ID group-ID smd/tlsph_shape :pre +compute ID group-ID smd/tlsph/shape :pre ID, group-ID are documented in "compute"_compute.html command -smd/tlsph_shape = style name of this compute command :ul +smd/tlsph/shape = style name of this compute command :ul [Examples:] -compute 1 all smd/tlsph_shape :pre +compute 1 all smd/tlsph/shape :pre [Description:] -Define a computation that outputs the current shape of the volume associated with a particle as a rotated ellipsoid. -It is only meaningful for particles which interact according to the Total-Lagrangian SPH pair style. +Define a computation that outputs the current shape of the volume +associated with a particle as a rotated ellipsoid. It is only +meaningful for particles which interact according to the +Total-Lagrangian SPH pair style. -See "this PDF guide"_USER/smd/SMD_LAMMPS_userguide.pdf to use Smooth Mach Dynamics in LAMMPS. +See "this PDF guide"_USER/smd/SMD_LAMMPS_userguide.pdf to use Smooth +Mach Dynamics in LAMMPS. [Output info:] This compute calculates a per-particle vector of vectors, which can be -accessed by any command that uses per-particle values from a compute as input. See -"How-to discussions, section 6.15"_Section_howto.html#howto_15 -for an overview of LAMMPS output options. +accessed by any command that uses per-particle values from a compute +as input. See "How-to discussions, section +6.15"_Section_howto.html#howto_15 for an overview of LAMMPS output +options. -The per-particle vector has 7 entries. The first three entries correspond to the lengths of the ellipsoid's axes and have units of length. -These axis valus are computed as the contact radius times the xx, yy, or zz components of the Green-Lagrange strain tensor associated with the particle. -The next 4 values are quaternions (order: q, x, y, z) which describe the spatial rotation of the particle relative to its initial state. +The per-particle vector has 7 entries. The first three entries +correspond to the lengths of the ellipsoid's axes and have units of +length. These axis valus are computed as the contact radius times the +xx, yy, or zz components of the Green-Lagrange strain tensor +associated with the particle. The next 4 values are quaternions +(order: q, x, y, z) which describe the spatial rotation of the +particle relative to its initial state. [Restrictions:] -This compute is part of the USER-SMD package. It is only enabled if LAMMPS was -built with that package. See the "Making LAMMPS"_Section_start.html#start_3 -section for more info. +This compute is part of the USER-SMD package. It is only enabled if +LAMMPS was built with that package. See the "Making +LAMMPS"_Section_start.html#start_3 section for more info. -This quantity will be computed only for particles which interact with the Total-Lagrangian SPH pair style. +This quantity will be computed only for particles which interact with +the Total-Lagrangian SPH pair style. [Related commands:] -"smd/contact_radius"_compute_smd_contact_radius.html +"smd/contact/radius"_compute_smd_contact_radius.html [Default:] none diff --git a/doc/compute_smd_tlsph_strain.html b/doc/compute_smd_tlsph_strain.html index 609d031006..7b32c7d017 100644 --- a/doc/compute_smd_tlsph_strain.html +++ b/doc/compute_smd_tlsph_strain.html @@ -8,7 +8,7 @@ -compute 1 all smd/tlsph_shape +
compute 1 all smd/tlsph/shape
Description¶
-Define a computation that outputs the current shape of the volume associated with a particle as a rotated ellipsoid. -It is only meaningful for particles which interact according to the Total-Lagrangian SPH pair style.
-See this PDF guide to use Smooth Mach Dynamics in LAMMPS.
+Define a computation that outputs the current shape of the volume +associated with a particle as a rotated ellipsoid. It is only +meaningful for particles which interact according to the +Total-Lagrangian SPH pair style.
+See this PDF guide to use Smooth +Mach Dynamics in LAMMPS.
Output info:
This compute calculates a per-particle vector of vectors, which can be -accessed by any command that uses per-particle values from a compute as input. See -How-to discussions, section 6.15 -for an overview of LAMMPS output options.
-The per-particle vector has 7 entries. The first three entries correspond to the lengths of the ellipsoid’s axes and have units of length. -These axis valus are computed as the contact radius times the xx, yy, or zz components of the Green-Lagrange strain tensor associated with the particle. -The next 4 values are quaternions (order: q, x, y, z) which describe the spatial rotation of the particle relative to its initial state.
+accessed by any command that uses per-particle values from a compute +as input. See How-to discussions, section 6.15 for an overview of LAMMPS output +options. +The per-particle vector has 7 entries. The first three entries +correspond to the lengths of the ellipsoid’s axes and have units of +length. These axis valus are computed as the contact radius times the +xx, yy, or zz components of the Green-Lagrange strain tensor +associated with the particle. The next 4 values are quaternions +(order: q, x, y, z) which describe the spatial rotation of the +particle relative to its initial state.
Restrictions¶
-This compute is part of the USER-SMD package. It is only enabled if LAMMPS was -built with that package. See the Making LAMMPS -section for more info.
-This quantity will be computed only for particles which interact with the Total-Lagrangian SPH pair style.
+This compute is part of the USER-SMD package. It is only enabled if +LAMMPS was built with that package. See the Making LAMMPS section for more info.
+This quantity will be computed only for particles which interact with +the Total-Lagrangian SPH pair style.
compute smd/tlsph_strain command — LAMMPS documentation +compute smd/tlsph/strain command — LAMMPS documentation @@ -109,7 +109,7 @@- Docs » -
- compute smd/tlsph_strain command +
- compute smd/tlsph/strain command
-
@@ -125,48 +125,50 @@
-
compute smd/tlsph_strain command¶
+compute smd/tlsph/strain command¶
Syntax¶
-compute ID group-ID smd/tlsph_strain +
compute ID group-ID smd/tlsph/strain
- ID, group-ID are documented in compute command -
- smd/tlsph_strain = style name of this compute command +
- smd/tlsph/strain = style name of this compute command
Examples¶
-diff --git a/doc/compute_smd_tlsph_strain.txt b/doc/compute_smd_tlsph_strain.txt index 7624a90bda..68d446b3be 100644 --- a/doc/compute_smd_tlsph_strain.txt +++ b/doc/compute_smd_tlsph_strain.txt @@ -6,48 +6,53 @@ :line -compute smd/tlsph_strain command :h3 +compute smd/tlsph/strain command :h3 [Syntax:] -compute ID group-ID smd/tlsph_strain :pre +compute ID group-ID smd/tlsph/strain :pre ID, group-ID are documented in "compute"_compute.html command -smd/tlsph_strain = style name of this compute command :ul +smd/tlsph/strain = style name of this compute command :ul [Examples:] -compute 1 all smd/tlsph_strain :pre +compute 1 all smd/tlsph/strain :pre [Description:] -Define a computation that calculates the Green-Lagrange strain tensor for particles interacting via the Total-Lagrangian SPH pair style. +Define a computation that calculates the Green-Lagrange strain tensor +for particles interacting via the Total-Lagrangian SPH pair style. -See "this PDF guide"_USER/smd/SMD_LAMMPS_userguide.pdf to using Smooth Mach Dynamics in LAMMPS. +See "this PDF guide"_USER/smd/SMD_LAMMPS_userguide.pdf to using Smooth +Mach Dynamics in LAMMPS. [Output info:] This compute calculates a per-particle vector of vectors (tensors), which can be accessed by any command that uses per-particle values -from a compute as input. See -"How-to discussions, section 6.15"_Section_howto.html#howto_15 - for an overview of LAMMPS output options. +from a compute as input. See "How-to discussions, section +6.15"_Section_howto.html#howto_15 for an overview of LAMMPS output +options. -The per-particle tensor values will be given dimensionless. See "units"_units.html. +The per-particle tensor values will be given dimensionless. See +"units"_units.html. -The per-particle vector has 6 entries, corresponding to the xx, yy, zz, xy, xz, yz components -of the symmetric strain tensor. +The per-particle vector has 6 entries, corresponding to the xx, yy, +zz, xy, xz, yz components of the symmetric strain tensor. [Restrictions:] This compute is part of the USER-SMD package. It is only enabled if -LAMMPS was built with that package. See the "Making LAMMPS"_Section_start.html#start_3 -section for more info. +LAMMPS was built with that package. See the "Making +LAMMPS"_Section_start.html#start_3 section for more info. -This quantity will be computed only for particles which interact with the Total-Lagrangian SPH pair style. +This quantity will be computed only for particles which interact with +the Total-Lagrangian SPH pair style. [Related commands:] -"smd/tlsph_strain_rate"_compute_smd_tlsph_strain_rate.html, "smd/tlsph_stress"_compute_smd_tlsph_stress.html +"smd/tlsph/strain/rate"_compute_smd_tlsph_strain_rate.html, +"smd/tlsph/stress"_compute_smd_tlsph_stress.html [Default:] none diff --git a/doc/compute_smd_tlsph_strain_rate.html b/doc/compute_smd_tlsph_strain_rate.html index 87371c49d8..6697c2c69a 100644 --- a/doc/compute_smd_tlsph_strain_rate.html +++ b/doc/compute_smd_tlsph_strain_rate.html @@ -8,7 +8,7 @@ -compute 1 all smd/tlsph_strain +
compute 1 all smd/tlsph/strain
Description¶
-Define a computation that calculates the Green-Lagrange strain tensor for particles interacting via the Total-Lagrangian SPH pair style.
-See this PDF guide to using Smooth Mach Dynamics in LAMMPS.
+Define a computation that calculates the Green-Lagrange strain tensor +for particles interacting via the Total-Lagrangian SPH pair style.
+See this PDF guide to using Smooth +Mach Dynamics in LAMMPS.
Output info:
This compute calculates a per-particle vector of vectors (tensors), which can be accessed by any command that uses per-particle values -from a compute as input. See -How-to discussions, section 6.15
--
-for an overview of LAMMPS output options.The per-particle tensor values will be given dimensionless. See units.
-The per-particle vector has 6 entries, corresponding to the xx, yy, zz, xy, xz, yz components -of the symmetric strain tensor.
+from a compute as input. See How-to discussions, section 6.15 for an overview of LAMMPS output +options. +The per-particle tensor values will be given dimensionless. See +units.
+The per-particle vector has 6 entries, corresponding to the xx, yy, +zz, xy, xz, yz components of the symmetric strain tensor.
Restrictions¶
This compute is part of the USER-SMD package. It is only enabled if -LAMMPS was built with that package. See the Making LAMMPS -section for more info.
-This quantity will be computed only for particles which interact with the Total-Lagrangian SPH pair style.
+LAMMPS was built with that package. See the Making LAMMPS section for more info. +This quantity will be computed only for particles which interact with +the Total-Lagrangian SPH pair style.
Related commands¶
-smd/tlsph_strain_rate, smd/tlsph_stress
+smd/tlsph/strain/rate, +smd/tlsph/stress
Default: none
compute smd/tlsph_strain_rate command — LAMMPS documentation +compute smd/tlsph/strain/rate command — LAMMPS documentation @@ -109,7 +109,7 @@- Docs » -
- compute smd/tlsph_strain_rate command +
- compute smd/tlsph/strain/rate command
-
@@ -125,46 +125,48 @@
-
compute smd/tlsph_strain_rate command¶
+compute smd/tlsph/strain/rate command¶
Syntax¶
-compute ID group-ID smd/tlsph_strain_rate +
compute ID group-ID smd/tlsph/strain/rate
- ID, group-ID are documented in compute command -
- smd/tlsph_strain_rate = style name of this compute command +
- smd/tlsph/strain/rate = style name of this compute command
Examples¶
-diff --git a/doc/compute_smd_tlsph_strain_rate.txt b/doc/compute_smd_tlsph_strain_rate.txt index e9b81b709e..88224ea0e3 100644 --- a/doc/compute_smd_tlsph_strain_rate.txt +++ b/doc/compute_smd_tlsph_strain_rate.txt @@ -6,48 +6,52 @@ :line -compute smd/tlsph_strain_rate command :h3 +compute smd/tlsph/strain/rate command :h3 [Syntax:] -compute ID group-ID smd/tlsph_strain_rate :pre +compute ID group-ID smd/tlsph/strain/rate :pre ID, group-ID are documented in "compute"_compute.html command -smd/tlsph_strain_rate = style name of this compute command :ul +smd/tlsph/strain/rate = style name of this compute command :ul [Examples:] -compute 1 all smd/tlsph_strain_rate :pre +compute 1 all smd/tlsph/strain/rate :pre [Description:] -Define a computation that calculates the rate of the strain tensor for particles interacting via the Total-Lagrangian SPH pair style. +Define a computation that calculates the rate of the strain tensor for +particles interacting via the Total-Lagrangian SPH pair style. -See "this PDF guide"_USER/smd/SMD_LAMMPS_userguide.pdf to using Smooth Mach Dynamics in LAMMPS. +See "this PDF guide"_USER/smd/SMD_LAMMPS_userguide.pdf to using Smooth +Mach Dynamics in LAMMPS. [Output info:] -This compute calculates a per-particle vector of vectors (tensors), which can be -accessed by any command that uses per-particle values from a compute as input. See -"How-to discussions, section 6.15"_Section_howto.html#howto_15 -for an overview of LAMMPS output options. +This compute calculates a per-particle vector of vectors (tensors), +which can be accessed by any command that uses per-particle values +from a compute as input. See "How-to discussions, section +6.15"_Section_howto.html#howto_15 for an overview of LAMMPS output +options. The values will be given in "units"_units.html of one over time. -The per-particle vector has 6 entries, corresponding to the xx, yy, zz, xy, xz, yz components -of the symmetric strain rate tensor. +The per-particle vector has 6 entries, corresponding to the xx, yy, +zz, xy, xz, yz components of the symmetric strain rate tensor. [Restrictions:] This compute is part of the USER-SMD package. It is only enabled if -LAMMPS was built with that package. See the "Making LAMMPS"_Section_start.html#start_3 -section for more info. +LAMMPS was built with that package. See the "Making +LAMMPS"_Section_start.html#start_3 section for more info. - -This quantity will be computed only for particles which interact with Total-Lagrangian SPH pair style. +This quantity will be computed only for particles which interact with +Total-Lagrangian SPH pair style. [Related commands:] -"smd/tlsph_strain"_compute_smd_tlsph_strain.html, "smd/tlsph_stress"_compute_smd_tlsph_stress.html +"compute smd/tlsph/strain"_compute_smd_tlsph_strain.html, "compute +smd/tlsph/stress"_compute_smd_tlsph_stress.html [Default:] none diff --git a/doc/compute_smd_tlsph_stress.html b/doc/compute_smd_tlsph_stress.html index caf561594e..132a3e3358 100644 --- a/doc/compute_smd_tlsph_stress.html +++ b/doc/compute_smd_tlsph_stress.html @@ -8,7 +8,7 @@ -compute 1 all smd/tlsph_strain_rate +
compute 1 all smd/tlsph/strain/rate
Description¶
-Define a computation that calculates the rate of the strain tensor for particles interacting via the Total-Lagrangian SPH pair style.
-See this PDF guide to using Smooth Mach Dynamics in LAMMPS.
+Define a computation that calculates the rate of the strain tensor for +particles interacting via the Total-Lagrangian SPH pair style.
+See this PDF guide to using Smooth +Mach Dynamics in LAMMPS.
Output info:
-This compute calculates a per-particle vector of vectors (tensors), which can be -accessed by any command that uses per-particle values from a compute as input. See -How-to discussions, section 6.15 -for an overview of LAMMPS output options.
+This compute calculates a per-particle vector of vectors (tensors), +which can be accessed by any command that uses per-particle values +from a compute as input. See How-to discussions, section 6.15 for an overview of LAMMPS output +options.
The values will be given in units of one over time.
-The per-particle vector has 6 entries, corresponding to the xx, yy, zz, xy, xz, yz components -of the symmetric strain rate tensor.
+The per-particle vector has 6 entries, corresponding to the xx, yy, +zz, xy, xz, yz components of the symmetric strain rate tensor.
Restrictions¶
This compute is part of the USER-SMD package. It is only enabled if -LAMMPS was built with that package. See the Making LAMMPS -section for more info.
-This quantity will be computed only for particles which interact with Total-Lagrangian SPH pair style.
+LAMMPS was built with that package. See the Making LAMMPS section for more info. +This quantity will be computed only for particles which interact with +Total-Lagrangian SPH pair style.
Related commands¶
-smd/tlsph_strain, smd/tlsph_stress
+compute smd/tlsph/strain, compute smd/tlsph/stress
Default: none
compute smd/tlsph_stress command — LAMMPS documentation +compute smd/tlsph/stress command — LAMMPS documentation @@ -109,7 +109,7 @@- Docs » -
- compute smd/tlsph_stress command +
- compute smd/tlsph/stress command
-
@@ -125,47 +125,51 @@
-
compute smd/tlsph_stress command¶
+compute smd/tlsph/stress command¶
Syntax¶
-compute ID group-ID smd/tlsph_stress +
compute ID group-ID smd/tlsph/stress
- ID, group-ID are documented in compute command -
- smd/tlsph_stress = style name of this compute command +
- smd/tlsph/stress = style name of this compute command
Examples¶
-diff --git a/doc/compute_smd_tlsph_stress.txt b/doc/compute_smd_tlsph_stress.txt index 9c8dab6b0a..0929e5ea07 100644 --- a/doc/compute_smd_tlsph_stress.txt +++ b/doc/compute_smd_tlsph_stress.txt @@ -6,48 +6,54 @@ :line -compute smd/tlsph_stress command :h3 +compute smd/tlsph/stress command :h3 [Syntax:] -compute ID group-ID smd/tlsph_stress :pre +compute ID group-ID smd/tlsph/stress :pre ID, group-ID are documented in "compute"_compute.html command -smd/tlsph_stress = style name of this compute command :ul +smd/tlsph/stress = style name of this compute command :ul [Examples:] -compute 1 all smd/tlsph_stress :pre +compute 1 all smd/tlsph/stress :pre [Description:] -Define a computation that outputs the Cauchy stress tensor for particles interacting via the Total-Lagrangian SPH pair style. +Define a computation that outputs the Cauchy stress tensor for +particles interacting via the Total-Lagrangian SPH pair style. -See "this PDF guide"_USER/smd/SMD_LAMMPS_userguide.pdf to using Smooth Mach Dynamics in LAMMPS. +See "this PDF guide"_USER/smd/SMD_LAMMPS_userguide.pdf to using Smooth +Mach Dynamics in LAMMPS. [Output info:] This compute calculates a per-particle vector of vectors (tensors), which can be -accessed by any command that uses per-particle values from a compute as input. See +accessed by any command that uses per-particle values from a compute +as input. See "How-to discussions, section 6.15"_Section_howto.html#howto_15 for an overview of LAMMPS output options. The values will be given in "units"_units.html of pressure. -The per-particle vector has 7 entries. The first six entries correspond to the xx, yy, zz, xy, xz and yz components -of the symmetric Cauchy stress tensor. The seventh entry is the second invariant of the stress tensor, i.e., -the von Mises equivalent stress. +The per-particle vector has 7 entries. The first six entries +correspond to the xx, yy, zz, xy, xz and yz components of the +symmetric Cauchy stress tensor. The seventh entry is the second +invariant of the stress tensor, i.e., the von Mises equivalent stress. [Restrictions:] This compute is part of the USER-SMD package. It is only enabled if -LAMMPS was built with that package. See the "Making LAMMPS"_Section_start.html#start_3 -section for more info. +LAMMPS was built with that package. See the "Making +LAMMPS"_Section_start.html#start_3 section for more info. -This quantity will be computed only for particles which interact with the Total-Lagrangian SPH pair style. +This quantity will be computed only for particles which interact with +the Total-Lagrangian SPH pair style. [Related commands:] -"smd/tlsph_strain"_compute_smd_tlsph_strain.html, "smd/tlsph_strain_rate"_compute_smd_tlsph_strain_rate.html +"compute smd/tlsph/strain"_compute_smd_tlsph_strain.html, "cmopute +smd/tlsph/strain/rate"_compute_smd_tlsph_strain_rate.html [Default:] none diff --git a/doc/compute_smd_triangle_mesh_vertices.html b/doc/compute_smd_triangle_mesh_vertices.html index 2f7b81b6fc..dcae23cc84 100644 --- a/doc/compute_smd_triangle_mesh_vertices.html +++ b/doc/compute_smd_triangle_mesh_vertices.html @@ -8,7 +8,7 @@ -compute 1 all smd/tlsph_stress +
compute 1 all smd/tlsph/stress
Description¶
-Define a computation that outputs the Cauchy stress tensor for particles interacting via the Total-Lagrangian SPH pair style.
-See this PDF guide to using Smooth Mach Dynamics in LAMMPS.
+Define a computation that outputs the Cauchy stress tensor for +particles interacting via the Total-Lagrangian SPH pair style.
+See this PDF guide to using Smooth +Mach Dynamics in LAMMPS.
Output info:
This compute calculates a per-particle vector of vectors (tensors), which can be -accessed by any command that uses per-particle values from a compute as input. See +accessed by any command that uses per-particle values from a compute +as input. See How-to discussions, section 6.15 for an overview of LAMMPS output options.
The values will be given in units of pressure.
-The per-particle vector has 7 entries. The first six entries correspond to the xx, yy, zz, xy, xz and yz components -of the symmetric Cauchy stress tensor. The seventh entry is the second invariant of the stress tensor, i.e., -the von Mises equivalent stress.
+The per-particle vector has 7 entries. The first six entries +correspond to the xx, yy, zz, xy, xz and yz components of the +symmetric Cauchy stress tensor. The seventh entry is the second +invariant of the stress tensor, i.e., the von Mises equivalent stress.
Restrictions¶
This compute is part of the USER-SMD package. It is only enabled if -LAMMPS was built with that package. See the Making LAMMPS -section for more info.
-This quantity will be computed only for particles which interact with the Total-Lagrangian SPH pair style.
+LAMMPS was built with that package. See the Making LAMMPS section for more info. +This quantity will be computed only for particles which interact with +the Total-Lagrangian SPH pair style.
Related commands¶
-smd/tlsph_strain, smd/tlsph_strain_rate
+compute smd/tlsph/strain, cmopute smd/tlsph/strain/rate
Default: none
compute smd/triangle_mesh_vertices — LAMMPS documentation +compute smd/triangle/mesh/vertices — LAMMPS documentation @@ -109,7 +109,7 @@- Docs » -
- compute smd/triangle_mesh_vertices +
- compute smd/triangle/mesh/vertices
-
@@ -125,20 +125,20 @@
-
compute smd/triangle_mesh_vertices¶
+compute smd/triangle/mesh/vertices¶
Syntax¶
-compute ID group-ID smd/triangle_mesh_vertices +
compute ID group-ID smd/triangle/mesh/vertices
- ID, group-ID are documented in compute command -
- smd/triangle_mesh_vertices = style name of this compute command +
- smd/triangle/mesh/vertices = style name of this compute command
diff --git a/doc/compute_smd_triangle_mesh_vertices.txt b/doc/compute_smd_triangle_mesh_vertices.txt index 9d7740c7ec..7d0b4d0dbc 100644 --- a/doc/compute_smd_triangle_mesh_vertices.txt +++ b/doc/compute_smd_triangle_mesh_vertices.txt @@ -8,25 +8,27 @@ :line -compute smd/triangle_mesh_vertices :h3 +compute smd/triangle/mesh/vertices :h3 [Syntax:] -compute ID group-ID smd/triangle_mesh_vertices :pre +compute ID group-ID smd/triangle/mesh/vertices :pre ID, group-ID are documented in "compute"_compute.html command -smd/triangle_mesh_vertices = style name of this compute command :ul +smd/triangle/mesh/vertices = style name of this compute command :ul [Examples:] -compute 1 all smd/triangle_mesh_vertices :pre +compute 1 all smd/triangle/mesh/vertices :pre [Description:] Define a computation that returns the coordinates of the vertices -corresponding to the triangle-elements of a mesh created by the "fix smd/wall_surface"_ls. +corresponding to the triangle-elements of a mesh created by the "fix +smd/wall_surface"_ls. -See "this PDF guide"_USER/smd/SMD_LAMMPS_userguide.pdf to using Smooth Mach Dynamics in LAMMPS. +See "this PDF guide"_USER/smd/SMD_LAMMPS_userguide.pdf to using Smooth +Mach Dynamics in LAMMPS. [Output info:] @@ -35,25 +37,28 @@ accessed by any command that uses per-particle values from a compute as input. See "How-to discussions, section 6.15"_Section_howto.html#howto_15 for an overview of LAMMPS output options. -The per-particle vector has nine entries, (x1/y1/z1), (x2/y2/z2), and (x3/y3/z3) corresponding -to the first, second, and third vertex of each triangle. +The per-particle vector has nine entries, (x1/y1/z1), (x2/y2/z2), and +(x3/y3/z3) corresponding to the first, second, and third vertex of +each triangle. -It is only meaningful to use this compute for a group of particles which is created via the -"fix smd/wall_surface"_ls command. +It is only meaningful to use this compute for a group of particles +which is created via the "fix smd/wall_surface"_ls command. -The output of this compute can be used with the dump2vtk_tris tool to generate a VTK representation of the -smd/wall_surace mesh for visualization purposes. +The output of this compute can be used with the dump2vtk_tris tool to +generate a VTK representation of the smd/wall_surace mesh for +visualization purposes. The values will be given in "units"_units.html of distance. [Restrictions:] This compute is part of the USER-SMD package. It is only enabled if -LAMMPS was built with that package. See the "Making LAMMPS"_Section_start.html#start_3 -section for more info. +LAMMPS was built with that package. See the "Making +LAMMPS"_Section_start.html#start_3 section for more info. [Related commands:] -"smd/move_tri_surf"_fix_smd_move_triangulated_surface.html, "smd/wall_surface"_ls +"compute smd/move/tri/surf"_fix_smd_move_triangulated_surface.html, +"compute smd/wall/surface"_ls [Default:] none diff --git a/doc/compute_smd_ulsph_num_neighs.html b/doc/compute_smd_ulsph_num_neighs.html index 2bb812f4bd..4bd0c2bd23 100644 --- a/doc/compute_smd_ulsph_num_neighs.html +++ b/doc/compute_smd_ulsph_num_neighs.html @@ -8,7 +8,7 @@ -Examples¶
-@@ -146,29 +146,32 @@compute 1 all smd/triangle_mesh_vertices +
compute 1 all smd/triangle/mesh/vertices
Description¶
Define a computation that returns the coordinates of the vertices corresponding to the triangle-elements of a mesh created by the `fix smd/wall_surface <ls_>`_.
-See this PDF guide to using Smooth Mach Dynamics in LAMMPS.
+See this PDF guide to using Smooth +Mach Dynamics in LAMMPS.
Output info:
This compute returns a per-particle vector of vectors, which can be accessed by any command that uses per-particle values from a compute as input. See How-to discussions, section 6.15 for an overview of LAMMPS output options.
-The per-particle vector has nine entries, (x1/y1/z1), (x2/y2/z2), and (x3/y3/z3) corresponding -to the first, second, and third vertex of each triangle.
-It is only meaningful to use this compute for a group of particles which is created via the -`fix smd/wall_surface <ls_>`_ command.
-The output of this compute can be used with the dump2vtk_tris tool to generate a VTK representation of the -smd/wall_surace mesh for visualization purposes.
+The per-particle vector has nine entries, (x1/y1/z1), (x2/y2/z2), and +(x3/y3/z3) corresponding to the first, second, and third vertex of +each triangle.
+It is only meaningful to use this compute for a group of particles +which is created via the `fix smd/wall_surface <ls_>`_ command.
+The output of this compute can be used with the dump2vtk_tris tool to +generate a VTK representation of the smd/wall_surace mesh for +visualization purposes.
The values will be given in units of distance.
Restrictions¶
This compute is part of the USER-SMD package. It is only enabled if -LAMMPS was built with that package. See the Making LAMMPS -section for more info.
+LAMMPS was built with that package. See the Making LAMMPS section for more info.Related commands¶
-smd/move_tri_surf, `smd/wall_surface <ls_>`_
+compute smd/move/tri/surf, +`compute smd/wall/surface <ls_>`_
Default: none
compute smd/ulsph_num_neighs command — LAMMPS documentation +compute smd/ulsph/num/neighs command — LAMMPS documentation @@ -109,7 +109,7 @@- Docs » -
- compute smd/ulsph_num_neighs command +
- compute smd/ulsph/num/neighs command
-
@@ -125,44 +125,47 @@
-
compute smd/ulsph_num_neighs command¶
+compute smd/ulsph/num/neighs command¶
Syntax¶
-compute ID group-ID smd/ulsph_num_neighs +
compute ID group-ID smd/ulsph/num/neighs
- ID, group-ID are documented in compute command -
- smd/ulsph_num_neighs = style name of this compute command +
- smd/ulsph/num/neighs = style name of this compute command
Examples¶
-diff --git a/doc/compute_smd_ulsph_num_neighs.txt b/doc/compute_smd_ulsph_num_neighs.txt index 00020f13c5..29eb32d5b1 100644 --- a/doc/compute_smd_ulsph_num_neighs.txt +++ b/doc/compute_smd_ulsph_num_neighs.txt @@ -6,31 +6,33 @@ :line -compute smd/ulsph_num_neighs command :h3 +compute smd/ulsph/num/neighs command :h3 [Syntax:] -compute ID group-ID smd/ulsph_num_neighs :pre +compute ID group-ID smd/ulsph/num/neighs :pre ID, group-ID are documented in "compute"_compute.html command -smd/ulsph_num_neighs = style name of this compute command :ul +smd/ulsph/num/neighs = style name of this compute command :ul [Examples:] -compute 1 all smd/ulsph_num_neighs :pre +compute 1 all smd/ulsph/num/neighs :pre [Description:] Define a computation that returns the number of neighbor particles -inside of the smoothing kernel radius for particles interacting via the updated Lagrangian SPH pair style. +inside of the smoothing kernel radius for particles interacting via +the updated Lagrangian SPH pair style. -See "this PDF guide"_USER/smd/SMD_LAMMPS_userguide.pdf to using Smooth Mach Dynamics in LAMMPS. +See "this PDF guide"_USER/smd/SMD_LAMMPS_userguide.pdf to using Smooth +Mach Dynamics in LAMMPS. [Output info:] This compute returns a per-particle vector, which can be accessed by -any command that uses per-particle values from a compute as input. See -"Section_howto 15"_Section_howto.html#howto_15 for an overview of +any command that uses per-particle values from a compute as input. +See "Section_howto 15"_Section_howto.html#howto_15 for an overview of LAMMPS output options. The per-particle values will be given dimentionless, see "units"_units.html. @@ -38,11 +40,13 @@ The per-particle values will be given dimentionless, see "units"_units.html. [Restrictions:] This compute is part of the USER-SMD package. It is only enabled if -LAMMPS was built with that package. See the "Making LAMMPS"_Section_start.html#start_2 -section for more info. This compute can only be used for particles which interact with the updated Lagrangian SPH pair style. +LAMMPS was built with that package. See the "Making +LAMMPS"_Section_start.html#start_2 section for more info. This compute +can only be used for particles which interact with the updated +Lagrangian SPH pair style. [Related commands:] -smd/tlsph_num_neighs +"compute smd/tlsph/num/neighs"_compute_smd_tlsph_num_neighs.html [Default:] none diff --git a/doc/compute_smd_ulsph_strain.html b/doc/compute_smd_ulsph_strain.html index 4376345123..6bf7b2a8a2 100644 --- a/doc/compute_smd_ulsph_strain.html +++ b/doc/compute_smd_ulsph_strain.html @@ -8,7 +8,7 @@ -compute 1 all smd/ulsph_num_neighs +
compute 1 all smd/ulsph/num/neighs
Description¶
Define a computation that returns the number of neighbor particles -inside of the smoothing kernel radius for particles interacting via the updated Lagrangian SPH pair style.
-See this PDF guide to using Smooth Mach Dynamics in LAMMPS.
+inside of the smoothing kernel radius for particles interacting via +the updated Lagrangian SPH pair style. +See this PDF guide to using Smooth +Mach Dynamics in LAMMPS.
Output info:
This compute returns a per-particle vector, which can be accessed by -any command that uses per-particle values from a compute as input. See -Section_howto 15 for an overview of +any command that uses per-particle values from a compute as input. +See Section_howto 15 for an overview of LAMMPS output options.
The per-particle values will be given dimentionless, see units.
Restrictions¶
This compute is part of the USER-SMD package. It is only enabled if -LAMMPS was built with that package. See the Making LAMMPS -section for more info. This compute can only be used for particles which interact with the updated Lagrangian SPH pair style.
+LAMMPS was built with that package. See the Making LAMMPS section for more info. This compute +can only be used for particles which interact with the updated +Lagrangian SPH pair style.compute smd/ulsph_strain command — LAMMPS documentation +compute smd/ulsph/strain command — LAMMPS documentation @@ -109,7 +109,7 @@- Docs » -
- compute smd/ulsph_strain command +
- compute smd/ulsph/strain command
-
@@ -125,46 +125,49 @@
-
compute smd/ulsph_strain command¶
+compute smd/ulsph/strain command¶
Syntax¶
-compute ID group-ID smd/ulsph_strain +
compute ID group-ID smd/ulsph/strain
- ID, group-ID are documented in compute command -
- smd/ulsph_strain = style name of this compute command +
- smd/ulsph/strain = style name of this compute command
Examples¶
-diff --git a/doc/compute_smd_ulsph_strain.txt b/doc/compute_smd_ulsph_strain.txt index e8418389d8..5a36515e84 100644 --- a/doc/compute_smd_ulsph_strain.txt +++ b/doc/compute_smd_ulsph_strain.txt @@ -6,46 +6,50 @@ :line -compute smd/ulsph_strain command :h3 +compute smd/ulsph/strain command :h3 [Syntax:] -compute ID group-ID smd/ulsph_strain :pre +compute ID group-ID smd/ulsph/strain :pre ID, group-ID are documented in "compute"_compute.html command -smd/ulsph_strain = style name of this compute command :ul +smd/ulsph/strain = style name of this compute command :ul [Examples:] -compute 1 all smd/ulsph_strain :pre +compute 1 all smd/ulsph/strain :pre [Description:] -Define a computation that outputs the logarithmic strain tensor. -for particles interacting via the updated Lagrangian SPH pair style. +Define a computation that outputs the logarithmic strain tensor. for +particles interacting via the updated Lagrangian SPH pair style. -See "this PDF guide"_USER/smd/SMD_LAMMPS_userguide.pdf to using Smooth Mach Dynamics in LAMMPS. +See "this PDF guide"_USER/smd/SMD_LAMMPS_userguide.pdf to using Smooth +Mach Dynamics in LAMMPS. [Output info:] -This compute calculates a per-particle tensor, which can be accessed by -any command that uses per-particle values from a compute as input. See -"Section_howto 15"_Section_howto.html#howto_15 for an overview of +This compute calculates a per-particle tensor, which can be accessed +by any command that uses per-particle values from a compute as input. +See "Section_howto 15"_Section_howto.html#howto_15 for an overview of LAMMPS output options. -The per-particle vector has 6 entries, corresponding to the xx, yy, zz, xy, xz, yz components -of the symmetric strain rate tensor. +The per-particle vector has 6 entries, corresponding to the xx, yy, +zz, xy, xz, yz components of the symmetric strain rate tensor. -The per-particle tensor values will be given dimensionless, see "units"_units.html. +The per-particle tensor values will be given dimensionless, see +"units"_units.html. [Restrictions:] This compute is part of the USER-SMD package. It is only enabled if -LAMMPS was built with that package. See the "Making LAMMPS"_Section_start.html#start_3 -section for more info. This compute can only be used for particles which interact with the updated Lagrangian SPH pair style. +LAMMPS was built with that package. See the "Making +LAMMPS"_Section_start.html#start_3 section for more info. This compute +can only be used for particles which interact with the updated +Lagrangian SPH pair style. [Related commands:] -smd/tlsph_strain +"compute smd/tlsph/strain"_compute_smd_tlsph_strain.html [Default:] none diff --git a/doc/compute_smd_ulsph_strain_rate.html b/doc/compute_smd_ulsph_strain_rate.html index ae12a1af32..411729b561 100644 --- a/doc/compute_smd_ulsph_strain_rate.html +++ b/doc/compute_smd_ulsph_strain_rate.html @@ -8,7 +8,7 @@ -compute 1 all smd/ulsph_strain +
compute 1 all smd/ulsph/strain
Description¶
-Define a computation that outputs the logarithmic strain tensor. -for particles interacting via the updated Lagrangian SPH pair style.
-See this PDF guide to using Smooth Mach Dynamics in LAMMPS.
+Define a computation that outputs the logarithmic strain tensor. for +particles interacting via the updated Lagrangian SPH pair style.
+See this PDF guide to using Smooth +Mach Dynamics in LAMMPS.
Output info:
-This compute calculates a per-particle tensor, which can be accessed by -any command that uses per-particle values from a compute as input. See -Section_howto 15 for an overview of +
This compute calculates a per-particle tensor, which can be accessed +by any command that uses per-particle values from a compute as input. +See Section_howto 15 for an overview of LAMMPS output options.
-The per-particle vector has 6 entries, corresponding to the xx, yy, zz, xy, xz, yz components -of the symmetric strain rate tensor.
-The per-particle tensor values will be given dimensionless, see units.
+The per-particle vector has 6 entries, corresponding to the xx, yy, +zz, xy, xz, yz components of the symmetric strain rate tensor.
+The per-particle tensor values will be given dimensionless, see +units.
Restrictions¶
This compute is part of the USER-SMD package. It is only enabled if -LAMMPS was built with that package. See the Making LAMMPS -section for more info. This compute can only be used for particles which interact with the updated Lagrangian SPH pair style.
+LAMMPS was built with that package. See the Making LAMMPS section for more info. This compute +can only be used for particles which interact with the updated +Lagrangian SPH pair style.compute smd/ulsph_strain_rate command — LAMMPS documentation +compute smd/ulsph/strain/rate command — LAMMPS documentation @@ -109,7 +109,7 @@- Docs » -
- compute smd/ulsph_strain_rate command +
- compute smd/ulsph/strain/rate command
-
@@ -125,46 +125,49 @@
-
compute smd/ulsph_strain_rate command¶
+compute smd/ulsph/strain/rate command¶
Syntax¶
-compute ID group-ID smd/ulsph_strain_rate +
compute ID group-ID smd/ulsph/strain/rate
- ID, group-ID are documented in compute command -
- smd/ulsph_strain_rate = style name of this compute command +
- smd/ulsph/strain/rate = style name of this compute command
Examples¶
-diff --git a/doc/compute_smd_ulsph_strain_rate.txt b/doc/compute_smd_ulsph_strain_rate.txt index 4d5fb952cb..3f32e43912 100644 --- a/doc/compute_smd_ulsph_strain_rate.txt +++ b/doc/compute_smd_ulsph_strain_rate.txt @@ -6,47 +6,51 @@ :line -compute smd/ulsph_strain_rate command :h3 +compute smd/ulsph/strain/rate command :h3 [Syntax:] -compute ID group-ID smd/ulsph_strain_rate :pre +compute ID group-ID smd/ulsph/strain/rate :pre ID, group-ID are documented in "compute"_compute.html command -smd/ulsph_strain_rate = style name of this compute command :ul +smd/ulsph/strain/rate = style name of this compute command :ul [Examples:] -compute 1 all smd/ulsph_strain_rate :pre +compute 1 all smd/ulsph/strain/rate :pre [Description:] -Define a computation that outputs the rate of the logarithmic strain tensor -for particles interacting via the updated Lagrangian SPH pair style. +Define a computation that outputs the rate of the logarithmic strain +tensor for particles interacting via the updated Lagrangian SPH pair +style. -See "this PDF guide"_USER/smd/SMD_LAMMPS_userguide.pdf to using Smooth Mach Dynamics in LAMMPS. +See "this PDF guide"_USER/smd/SMD_LAMMPS_userguide.pdf to using Smooth +Mach Dynamics in LAMMPS. [Output info:] -This compute calculates a per-particle vector of vectors (tensors), which -can be accessed by any command that uses per-particle values from a compute -as input. See "Section_howto 15"_Section_howto.html#howto_15 for an overview of -LAMMPS output options. +This compute calculates a per-particle vector of vectors (tensors), +which can be accessed by any command that uses per-particle values +from a compute as input. See "Section_howto +15"_Section_howto.html#howto_15 for an overview of LAMMPS output +options. The values will be given in "units"_units.html of one over time. -The per-particle vector has 6 entries, corresponding to the xx, yy, zz, xy, xz, yz components -of the symmetric strain rate tensor. +The per-particle vector has 6 entries, corresponding to the xx, yy, +zz, xy, xz, yz components of the symmetric strain rate tensor. [Restrictions:] This compute is part of the USER-SMD package. It is only enabled if -LAMMPS was built with that package. See the "Making LAMMPS"_Section_start.html#start_2 -section for more info. This compute can only be used for particles which interact with the updated Lagrangian SPH pair style. - +LAMMPS was built with that package. See the "Making +LAMMPS"_Section_start.html#start_2 section for more info. This compute +can only be used for particles which interact with the updated +Lagrangian SPH pair style. [Related commands:] -smd/utsph_strain_rate +"compute smd/tlsph/strain/rate"_compute_smd_tlsph_strain_rate.html [Default:] none diff --git a/doc/compute_smd_ulsph_stress.html b/doc/compute_smd_ulsph_stress.html index 59938884a1..9fdb828801 100644 --- a/doc/compute_smd_ulsph_stress.html +++ b/doc/compute_smd_ulsph_stress.html @@ -8,7 +8,7 @@ -compute 1 all smd/ulsph_strain_rate +
compute 1 all smd/ulsph/strain/rate
Description¶
-Define a computation that outputs the rate of the logarithmic strain tensor -for particles interacting via the updated Lagrangian SPH pair style.
-See this PDF guide to using Smooth Mach Dynamics in LAMMPS.
+Define a computation that outputs the rate of the logarithmic strain +tensor for particles interacting via the updated Lagrangian SPH pair +style.
+See this PDF guide to using Smooth +Mach Dynamics in LAMMPS.
Output info:
-This compute calculates a per-particle vector of vectors (tensors), which -can be accessed by any command that uses per-particle values from a compute -as input. See Section_howto 15 for an overview of -LAMMPS output options.
+This compute calculates a per-particle vector of vectors (tensors), +which can be accessed by any command that uses per-particle values +from a compute as input. See Section_howto 15 for an overview of LAMMPS output +options.
The values will be given in units of one over time.
-The per-particle vector has 6 entries, corresponding to the xx, yy, zz, xy, xz, yz components -of the symmetric strain rate tensor.
+The per-particle vector has 6 entries, corresponding to the xx, yy, +zz, xy, xz, yz components of the symmetric strain rate tensor.
Restrictions¶
This compute is part of the USER-SMD package. It is only enabled if -LAMMPS was built with that package. See the Making LAMMPS -section for more info. This compute can only be used for particles which interact with the updated Lagrangian SPH pair style.
+LAMMPS was built with that package. See the Making LAMMPS section for more info. This compute +can only be used for particles which interact with the updated +Lagrangian SPH pair style.compute smd/ulsph_stress command — LAMMPS documentation +compute smd/ulsph/stress command — LAMMPS documentation @@ -109,7 +109,7 @@- Docs » -
- compute smd/ulsph_stress command +
- compute smd/ulsph/stress command
-
@@ -125,49 +125,49 @@
-
compute smd/ulsph_stress command¶
+compute smd/ulsph/stress command¶
Syntax¶
-diff --git a/doc/compute_smd_vol.txt b/doc/compute_smd_vol.txt index 1e0ab786bf..239ab1a1d5 100644 --- a/doc/compute_smd_vol.txt +++ b/doc/compute_smd_vol.txt @@ -21,32 +21,33 @@ compute 1 all smd/vol :pre [Description:] -Define a computation that provides the per-particle volume and the sum of the per-particle volumes of the -group for which the fix is defined. +Define a computation that provides the per-particle volume and the sum +of the per-particle volumes of the group for which the fix is defined. -See "this PDF guide"_USER/smd/SMD_LAMMPS_userguide.pdf to using Smooth Mach Dynamics in -LAMMPS. +See "this PDF guide"_USER/smd/SMD_LAMMPS_userguide.pdf to using Smooth +Mach Dynamics in LAMMPS. [Output info:] -This compute calculates a per-particle vector, which can be accessed by -any command that uses per-particle values from a compute as input. See -"How-to discussions, section 6.15"_Section_howto.html#howto_15 -for an overview of LAMMPS output options. +This compute calculates a per-particle vector, which can be accessed +by any command that uses per-particle values from a compute as input. +See "How-to discussions, section 6.15"_Section_howto.html#howto_15 for +an overview of LAMMPS output options. -The per-particle vector values will be given in "units"_units.html of volume. +The per-particle vector values will be given in "units"_units.html of +volume. -Additionally, the compute returns a scalar, which is the sum of the per-particle volumes of the -group for which the fix is defined. +Additionally, the compute returns a scalar, which is the sum of the +per-particle volumes of the group for which the fix is defined. [Restrictions:] This compute is part of the USER-SMD package. It is only enabled if -LAMMPS was built with that package. See the "Making LAMMPS"_Section_start.html#start_3 - section for more info. +LAMMPS was built with that package. See the "Making +LAMMPS"_Section_start.html#start_3 section for more info. [Related commands:] -"smd/rho"_compute_smd_rho.html +"compute smd/rho"_compute_smd_rho.html [Default:] none diff --git a/doc/genindex.html b/doc/genindex.html index 3610284fde..a04e004eab 100644 --- a/doc/genindex.html +++ b/doc/genindex.html @@ -578,7 +578,7 @@ -compute ID group-ID smd/ulsph_stress +
compute ID group-ID smd/ulsph/stress
- ID, group-ID are documented in compute command -
- smd/ulsph_stress = style name of this compute command +
- smd/ulsph/stress = style name of this compute command
Examples¶
-diff --git a/doc/compute_smd_ulsph_stress.txt b/doc/compute_smd_ulsph_stress.txt index 84a987a8e7..4d1994e37c 100644 --- a/doc/compute_smd_ulsph_stress.txt +++ b/doc/compute_smd_ulsph_stress.txt @@ -6,48 +6,53 @@ :line -compute smd/ulsph_stress command :h3 +compute smd/ulsph/stress command :h3 [Syntax:] -compute ID group-ID smd/ulsph_stress :pre +compute ID group-ID smd/ulsph/stress :pre ID, group-ID are documented in "compute"_compute.html command -smd/ulsph_stress = style name of this compute command :ul +smd/ulsph/stress = style name of this compute command :ul [Examples:] -compute 1 all smd/ulsph_stress :pre +compute 1 all smd/ulsph/stress :pre [Description:] Define a computation that outputs the Cauchy stress tensor. -See "this PDF guide"_USER/smd/SMD_LAMMPS_userguide.pdf to using Smooth Mach Dynamics in LAMMPS. +See "this PDF guide"_USER/smd/SMD_LAMMPS_userguide.pdf to using Smooth +Mach Dynamics in LAMMPS. [Output info:] This compute calculates a per-particle vector of vectors (tensors), which can be accessed by any command that uses per-particle values -from a compute as input. See "Section_howto 15"_Section_howto.html#howto_15 -for an overview of LAMMPS output options. +from a compute as input. See "Section_howto +15"_Section_howto.html#howto_15 for an overview of LAMMPS output +options. The values will be given in "units"_units.html of pressure. -The per-particle vector has 7 entries. The first six entries correspond to the xx, yy, zz, xy, xz, yz components -of the symmetric Cauchy stress tensor. The seventh entry is the second invariant of the stress tensor, i.e., -the von Mises equivalent stress. +The per-particle vector has 7 entries. The first six entries +correspond to the xx, yy, zz, xy, xz, yz components of the symmetric +Cauchy stress tensor. The seventh entry is the second invariant of the +stress tensor, i.e., the von Mises equivalent stress. [Restrictions:] This compute is part of the USER-SMD package. It is only enabled if -LAMMPS was built with that package. See the "Making LAMMPS"_Section_start.html#start_3 -section for more info. This compute can only be used for particles which interact with the updated Lagrangian SPH pair style. - +LAMMPS was built with that package. See the "Making +LAMMPS"_Section_start.html#start_3 section for more info. This compute +can only be used for particles which interact with the updated +Lagrangian SPH pair style. [Related commands:] -"smd/ulsph_strain"_compute_smd_ulsph_strain.html, "smd/ulsph_strain_rate"_compute_smd_ulsph_strain_rate.html -"smd/tlsph_stress"_compute_smd_tlsph_stress.html :pre +"compute smd/ulsph/strain"_compute_smd_ulsph_strain.html, "compute +smd/ulsph/strain/rate"_compute_smd_ulsph_strain_rate.html "compute +smd/tlsph/stress"_compute_smd_tlsph_stress.html [Default:] none diff --git a/doc/compute_smd_vol.html b/doc/compute_smd_vol.html index 6d8d7b596d..9395cd0499 100644 --- a/doc/compute_smd_vol.html +++ b/doc/compute_smd_vol.html @@ -144,29 +144,28 @@compute 1 all smd/ulsph_stress +
compute 1 all smd/ulsph/stress
Description¶
Define a computation that outputs the Cauchy stress tensor.
-See this PDF guide to using Smooth Mach Dynamics in LAMMPS.
+See this PDF guide to using Smooth +Mach Dynamics in LAMMPS.
Output info:
This compute calculates a per-particle vector of vectors (tensors), which can be accessed by any command that uses per-particle values -from a compute as input. See Section_howto 15 -for an overview of LAMMPS output options.
+from a compute as input. See Section_howto 15 for an overview of LAMMPS output +options.The values will be given in units of pressure.
-The per-particle vector has 7 entries. The first six entries correspond to the xx, yy, zz, xy, xz, yz components -of the symmetric Cauchy stress tensor. The seventh entry is the second invariant of the stress tensor, i.e., -the von Mises equivalent stress.
+The per-particle vector has 7 entries. The first six entries +correspond to the xx, yy, zz, xy, xz, yz components of the symmetric +Cauchy stress tensor. The seventh entry is the second invariant of the +stress tensor, i.e., the von Mises equivalent stress.
Restrictions¶
This compute is part of the USER-SMD package. It is only enabled if -LAMMPS was built with that package. See the Making LAMMPS -section for more info. This compute can only be used for particles which interact with the updated Lagrangian SPH pair style.
+LAMMPS was built with that package. See the Making LAMMPS section for more info. This compute +can only be used for particles which interact with the updated +Lagrangian SPH pair style.Related commands¶
--smd/ulsph_strain, smd/ulsph_strain_rate -smd/tlsph_stress -
+compute smd/ulsph/strain, compute smd/ulsph/strain/rate compute smd/tlsph/stress
Default: none
Description¶
-Define a computation that provides the per-particle volume and the sum of the per-particle volumes of the -group for which the fix is defined.
-See this PDF guide to using Smooth Mach Dynamics in -LAMMPS.
+Define a computation that provides the per-particle volume and the sum +of the per-particle volumes of the group for which the fix is defined.
+See this PDF guide to using Smooth +Mach Dynamics in LAMMPS.
Output info:
-This compute calculates a per-particle vector, which can be accessed by -any command that uses per-particle values from a compute as input. See -How-to discussions, section 6.15 -for an overview of LAMMPS output options.
-The per-particle vector values will be given in units of volume.
-Additionally, the compute returns a scalar, which is the sum of the per-particle volumes of the -group for which the fix is defined.
+This compute calculates a per-particle vector, which can be accessed +by any command that uses per-particle values from a compute as input. +See How-to discussions, section 6.15 for +an overview of LAMMPS output options.
+The per-particle vector values will be given in units of +volume.
+Additionally, the compute returns a scalar, which is the sum of the +per-particle volumes of the group for which the fix is defined.
Restrictions¶
This compute is part of the USER-SMD package. It is only enabled if -LAMMPS was built with that package. See the Making LAMMPS
--
+LAMMPS was built with that package. See the Making LAMMPS section for more info.section for more info.- compute smd/contact_radius +
-- compute smd/contact/radius
@@ -586,19 +586,19 @@- compute smd/hourglass_error +
- compute smd/hourglass/error
-- compute smd/internal_energy +
- compute smd/internal/energy
-- compute smd/plastic_strain +
- compute smd/plastic/strain
-- compute smd/plastic_strain_rate +
-- compute smd/plastic/strain/rate
@@ -606,47 +606,47 @@- compute smd/tlsph_defgrad +
- compute smd/tlsph/defgrad
-- compute smd/tlsph_dt +
- compute smd/tlsph/dt
-- compute smd/tlsph_num_neighs +
- compute smd/tlsph/num/neighs
-- compute smd/tlsph_shape +
- compute smd/tlsph/shape
-- compute smd/tlsph_strain +
- compute smd/tlsph/strain
-- compute smd/tlsph_strain_rate +
- compute smd/tlsph/strain/rate
-- compute smd/tlsph_stress +
- compute smd/tlsph/stress
-- compute smd/ulsph_num_neighs +
- compute smd/ulsph/num/neighs
-- compute smd/ulsph_strain +
- compute smd/ulsph/strain
-- compute smd/ulsph_strain_rate +
- compute smd/ulsph/strain/rate
-- compute smd/ulsph_stress +
- compute smd/ulsph/stress
diff --git a/doc/searchindex.js b/doc/searchindex.js index 9a8ed11241..4cd7603b1e 100644 --- a/doc/searchindex.js +++ b/doc/searchindex.js @@ -1 +1 @@ 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8,299,300,312,326,336,349,355,361,362,363,365,366,367,370,395,416,417,424,466,467,469,471,472,474,477,479],affin:[16,17,18,220,370,386],afil:233,aforement:18,afresh:[287,477,495],afshar:391,after:[2,3,5,6,8,9,11,12,15,21,22,33,39,40,41,44,50,57,58,59,61,63,71,146,147,148,149,150,151,152,155,156,157,158,160,161,168,169,171,172,175,176,181,190,191,192,193,194,195,197,198,199,203,204,206,207,214,215,216,217,218,220,224,231,242,243,244,245,246,251,252,253,255,261,262,263,269,274,275,276,278,281,285,289,297,299,302,310,315,317,318,319,321,322,323,324,325,329,331,333,337,340,341,347,354,360,361,363,364,366,368,369,370,371,372,377,384,386,393,394,395,396,402,403,404,415,416,417,419,420,421,422,426,430,432,433,440,441,451,453,454,455,458,464,466,468,469,470,471,472,474,475,477,479,481,483,486,487,490,494,495,496,497,498,499],afterrun:477,afterward:3,afterword:41,ag1:167,ag2:167,again:[6,11,12,16,17,62,142,148,154,162,191,194,220,235,285,340,354,365,416,417,464,466,467,469,471,476,483,485,495,497],against:[11,12,13,64,221,365,432,433],aggreg:[6,12,65,68,69,79,93,110,117,235,251,297,299,312,464,496],aggress:[235,483],agilio:[9,13],agre:[3,8,188,363,372,404,433],agreement:[5,7],ahd:401,ahead:333,aidan:[0,5,7,9,13,358],aij:13,aim:6,airebo:[],ajaramil:[7,9,13],aka:193,akohlmei:[7,9,13,195,236],aktulga:[7,9,292,433],al2o3:440,al2o3_001:[120,300],al3:167,ala:[242,440],alain:9,alat:[280,419],alb:[430,453,455],albeit:298,albert:9,alchem:[87,162],alcohol:329,alcu:[371,377],alcu_eam:430,alderton:390,alejandr:[255,256],alessandro:13,algebra:422,algorithm:[0,1,6,7,8,9,41,61,194,203,214,217,220,242,244,245,269,282,290,299,302,321,322,326,329,334,361,362,363,367,370,395,417,422,437,439,464,466,483],alia:[12,16],alias:[1,356],aliceblu:194,align:[6,12,29,41,71,170,188,210,214,237,358,469,472,490],alkali:395,all:[0,1,2,3,5,6,7,8,9,11,12,13,14,15,16,17,18,22,33,37,39,40,41,42,44,50,54,55,57,59,60,61,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,156,161,162,163,164,165,166,167,168,169,170,171,172,174,176,181,187,188,191,192,193,194,195,197,198,199,200,202,203,204,205,206,207,208,209,210,211,212,213,214,215,216,217,218,219,220,221,223,224,225,226,227,228,229,231,232,233,234,235,236,237,238,239,240,241,242,243,244,245,248,250,251,253,255,256,257,258,259,260,261,262,263,264,265,266,267,268,269,270,272,273,274,275,276,277,278,279,280,281,282,284,285,286,287,288,289,290,291,292,294,295,296,297,298,299,300,301,302,303,304,305,306,310,311,313,314,315,316,317,318,321,322,323,324,325,326,327,328,329,331,332,333,334,335,336,337,338,339,340,341,345,350,353,354,355,356,357,358,360,363,364,365,366,367,369,370,371,372,373,375,376,377,378,380,381,382,383,384,386,387,390,391,392,393,394,395,396,397,398,399,400,401,402,403,404,405,406,407,408,409,411,415,416,417,418,419,420,421,422,423,424,425,426,427,429,430,431,432,433,434,435,440,441,442,443,444,445,446,447,448,449,450,451,452,453,454,455,456,457,458,459,461,462,463,464,466,467,468,469,470,471,472,473,474,476,477,478,479,480,481,482,483,484,486,487,488,490,494,495,496,497,498,499],allen:[29,87,390,398],allentildeslei:87,allign:3,allindex:338,alloc:[3,5,6,8,9,11,12,60,229,328,364,366,370,428,433,469,477],allocat:3,alloi:[],allosw:71,allow:[1,2,3,6,8,9,11,12,13,14,15,16,17,18,22,37,39,40,41,55,57,58,59,61,62,63,77,92,108,110,144,146,147,148,161,166,167,168,170,176,187,188,191,193,194,195,197,198,200,202,203,204,206,207,208,209,210,211,212,214,216,217,218,219,220,221,225,226,229,231,232,233,234,236,239,242,245,246,250,252,255,256,280,284,285,286,287,288,289,293,299,300,302,303,305,306,310,314,321,322,323,324,326,327,328,329,330,331,337,339,341,350,355,356,358,363,364,365,366,369,370,373,377,378,379,380,381,382,387,393,395,399,400,401,402,407,411,416,417,422,424,430,433,434,437,439,440,449,459,461,464,467,469,471,472,473,474,475,476,479,481,482,483,486,487,495,496],almost:[2,3,12,60,237,289,326,356,367,370,449],alo:387,alon:[6,7,217,295,432,433,467],alond:13,along:[6,8,9,12,29,40,71,87,120,166,167,168,190,191,193,206,217,237,242,243,247,252,254,289,299,302,303,307,311,312,321,325,326,332,335,337,358,361,362,363,365,387,390,399,402,405,407,411,419,432,433,452,469,472,479,480,495],alonso:[420,421],alpha:[6,12,51,198,242,281,289,290,294,363,371,374,378,387,391,393,394,396,401,406,407,419,425,429,454,456,487,490],alpha_:[],alpha_c:415,alpha_i:441,alpha_ialpha_j:[],alpha_lj:415,alphabet:[2,3,22,37,44,55,63,176,187,197,341,350,364,384,450,469],alphanumer:[3,63,197,288,296,339,364,495],alreadi:[3,7,8,9,12,16,17,18,42,168,169,171,192,202,206,210,211,214,216,220,246,287,289,314,337,364,365,391,400,402,409,417,449,459,462,465,469,470,474,479,495],also:[0,1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,22,29,36,37,38,39,40,41,42,44,54,5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[432,433],chi:[93,157,190,280,290,292,396,398,496],chiefli:431,child:8,chip:[7,12,17,18,370,482],chipot:219,chiral:349,chmod:[11,12],cho:419,chocol:[7,194],choic:[3,6,12,15,16,18,40,41,54,87,143,146,147,161,172,188,206,210,211,214,217,220,221,233,239,242,253,255,282,290,299,321,350,356,361,362,365,367,370,402,415,424,428,469,478,479,482,483,489,490,494],choos:[1,3,6,7,8,12,16,17,18,29,39,54,87,119,158,159,193,215,216,217,218,221,228,239,242,253,255,257,258,259,260,261,262,263,285,286,314,318,332,355,356,362,459,464,466,478,484],chose:[453,455],chosen:[2,3,6,12,17,142,168,171,180,188,193,199,204,218,221,228,231,232,240,242,253,255,260,282,285,296,314,318,321,322,327,329,330,336,356,357,362,370,395,399,406,409,435,453,464,478,483,490],chri:166,christian:[7,9,14,17],christoph:7,chunk:[],chunkid:[66,75,90,94,105,107,116,148,163,165,206],chute:[4,10,234],ciccotti:302,cieplak:[6,174,481],cii:207,cij:207,circl:[42,71,310],circular:[3,6,146,189],circumst:18,circumv:[92,108,294],citat:[],cite:[3,7,8,12,239,440],ckio:2,cko:2,cl1:167,clarendon:[29,390],clarifi:[7,453,455],clariti:339,clark:427,class2:[],classic:[0,3,5,6,7,8,9,229,282,289,294,326,351,395],classifi:[9,450,458],claus:467,clean:[6,12,14,15,17,477],cleanli:[468,498],clear:[],clearli:7,clebsch:142,clermont:[9,13],clever:473,click:[2,11,22,37,44,55,168,176,187,193,236,341,350,365,384,450],client:[236,238],climb:[254,365,483],clinic:[7,13],clo:[157,190,496],clock:[12,464,483],clockwis:332,close:[3,6,11,12,13,39,41,67,71,143,171,191,216,217,218,233,240,242,255,276,299,302,332,335,354,356,359,361,362,365,370,372,377,387,388,405,419,424,436,438,455,473,479,490,492],closer:[3,41,118,166,190,191,214,218,222,323,365],closest:[216,280,299,329,398,434,449,459],cloud:[440,490],clovertown:18,clsuter:72,clump1:[284,299],clump2:[284,299],clump3:[284,299],clump:299,cluster:[],clutter:[3,9],cmap:469,cmatrix:233,cmax:419,cmd:[11,12,282,480],cmdarg:11,cmin:419,cmm:[],cn1:207,cn2:207,cna:[],cnn:207,cnr:[9,13],cnt:[402,473],co2:[40,167,302,364],coars:[7,9,29,36,40,54,180,284,299,314,400,435,481],coarser:[356,495],coarsest:142,code:[],coeff:[3,7,8,12,21,22,33,44,50,174,175,176,181,340,341,347,384,402,406,424,437,439,442,469],coeffcient:469,coeffici:[],coefficienct:391,coefficient0:393,coefficient1:393,coeffieci:[6,374,405],coeffincientn:393,coexist:[9,231,395],cohes:[6,396,419],coincid:[124,335,382,416,417,464],colberg:192,cold:[6,153,231,235,366,490],coldest:322,coleman8:9,coleman:[9,120,167,300],colin:9,collabor:[7,8,9,15],collect:[3,6,7,8,9,13,40,42,66,75,83,90,94,99,105,107,116,148,156,163,165,168,191,194,206,219,245,251,284,294,297,299,337,355,364,366,385,469,476,482,488,499],collid:[225,314,336],colliex:167,collinear:[3,284],collis:[3,242,314,332,336,392,399,462],colllis:314,colloid:[],colombo:39,colon:[195,337,470],color1:194,color2:194,color:[3,9,41,191,193,194,214,232,289,294],column:[3,6,9,12,13,42,63,65,66,67,68,69,71,75,77,79,81,90,92,93,94,105,107,108,110,112,115,116,117,118,119,121,142,143,148,156,163,165,166,167,188,191,194,197,205,206,207,209,210,211,212,245,252,253,289,299,315,316,326,336,397,401,432,433,470,484,486,495],columnar:166,colvar:[],colvarmodul:12,com:[],comamnd:220,comand:217,comannd:370,comb3:[],comb:[],comb_1:291,comb_2:291,combiant:388,combin:[3,6,7,9,11,13,36,40,63,65,69,79,87,93,104,110,117,146,147,161,191,193,203,209,236,245,255,282,288,318,327,335,338,340,355,356,358,362,370,385,387,388,395,396,402,414,415,441,451,453,455,458,461,472,477,482,490,495],come:[],comfort:[12,13],comm:[0,3,11,12,61,73,192,236,238,239,356,365,370,391,424,429,452,471],comm_modifi:[],comm_modift:61,comm_styl:[],comm_world:11,command:[],comment:[2,7,11,12,38,56,174,188,191,240,299,326,364,365,371,393,394,396,406,419,426,433,440,441,451,452,453,454,455,458,466,467,469,490,495],commerci:7,commmand:[3,6,12,59,109,277,405,463,464,466,483,498],common:[],commonli:[3,6,12,17,25,57,59,106,108,170,191,193,195,351,400,409,441,453,455,469,472,481],commun:[1,3,6,7,8,10,11,12,14,15,16,18,40,41,58,61,62,71,166,171,172,193,194,214,215,216,218,219,220,236,238,242,244,245,246,255,281,288,290,291,292,299,314,326,337,353,355,366,367,368,370,392,428,466,467,478,479,495,497,499],communc:355,comp:[7,192,238,239,302,356,365,395,424,429,434,448,452,454],compact:[63,197,384,450],compani:[5,7],compar:[1,3,4,6,8,12,17,39,86,112,120,151,167,176,187,194,224,290,337,339,355,356,363,365,419,440,464,483,484,490,494],comparison:[],comparison_of_nvidia_graphics_processing_unit:14,compass:[7,21,22,37,43,44,55,175,176,187,340,341,350,383,450],compat:[3,5,7,8,9,11,12,13,17,18,41,71,119,121,179,191,195,199,205,206,207,209,210,211,212,214,281,293,318,321,328,331,334,355,370,403,422,424,452,466,467,495],compens:[6,215,216,297,366,395],compet:325,competit:356,compil:[3,7,8,9,10,12,13,14,15,16,17,18,19,166,191,192,193,195,236,325,356,370,422,469,470,474,495],compl:17,complain:[12,17],complement:419,complementari:[7,387,407],complet:[3,6,9,11,12,15,41,59,71,194,210,214,219,245,282,285,288,314,325,327,339,354,365,370,396,437,439,457,464,469,474,477,481,483,486,490,495],complex:[6,8,11,12,13,25,40,42,62,92,108,142,144,156,168,169,242,310,335,353,365,395,422,452,467,469,472,495],compli:[321,325],complic:[6,7,9,12,13,204,231,467],complier:12,compon:[3,6,8,12,61,63,66,67,73,81,88,89,90,91,92,94,95,98,105,106,107,108,109,110,111,112,114,115,119,129,132,133,134,135,138,139,140,142,143,145,146,147,148,149,150,151,152,153,154,155,156,157,158,160,161,163,164,165,190,191,193,194,200,201,205,206,207,208,209,210,211,212,213,217,218,220,221,226,229,234,238,239,242,245,247,251,252,254,255,256,260,261,262,263,274,275,276,278,279,281,282,283,286,297,299,301,302,303,307,308,311,314,317,318,319,321,328,329,334,335,336,355,358,362,363,364,365,370,376,391,395,399,416,417,437,439,440,441,469,470,479,487,495,496],componenet:6,composit:[6,204,242,393],compound:[386,395,396,458],compres:[71,116,206],compress:[],compris:[40,335,434,457],compton:[120,167],comptu:3,compuat:356,comput:[],computation:[3,6,215,216,326,377],computational:490,compute_arrai:8,compute_fep:[199,415],compute_group_group:231,compute_inn:8,compute_ke_atom:8,compute_loc:8,compute_modifi:[],compute_peratom:8,compute_sa:[120,300],compute_scalar:8,compute_temp:8,compute_ti:199,compute_vector:8,compute_xrd:167,concaten:[2,3,498],concav:335,concentr:[71,393],concept:[6,148,158,206,478],conceptu:[3,6,71,156,218,220,365,387,402,419,474],concern:[6,73,87,192,232],concetr:71,concis:[11,325],conclud:12,concret:8,concurr:[9,16,356,495],conden:[326,453,455],condens:[6,150,326,372,389,393,407,458],condit:[],conducit:6,conduct:[],cone:472,confer:422,confid:[3,483],config:[12,191,466],configfil:219,configur:[1,2,6,12,15,17,38,59,124,170,188,190,191,193,197,218,219,220,221,225,231,238,239,269,282,290,325,353,363,365,372,377,394,419,422,451,453,455,458,464,469,471,472,483],confin:[469,483],conflict:[3,12,40,424,467],conform:[3,6,13,59,217,218,254,298,303,325,349,365,395,481],confus:[3,458],conjuct:391,conjug:[7,8,239,362,395,432,433],conjunct:[6,7,71,86,87,116,151,156,162,168,172,194,198,199,239,242,246,269,285,286,290,291,292,294,299,314,322,329,334,355,356,365,378,380,384,387,391,395,401,407,424,427,435,456,469,472,476,490,499],connect:[3,6,87,153,171,217,236,284,299,302,311,365,388,399,449,455,466,467,473,490],conput:3,consecut:[3,11,12,39,71,168,194,198,199,221,236,237,387,407,411,464,470,472],consequ:[1,6,204,326,406,483],conserv:[3,29,197,204,217,224,225,232,235,239,241,242,246,251,253,255,269,299,302,317,318,322,329,330,334,365,390,391,399,413,440,478,483],consid:[6,9,70,71,78,87,117,150,153,154,171,191,194,198,199,205,207,210,214,216,217,221,243,256,281,299,321,322,325,326,329,356,384,395,402,433,434,440,449,464,465,467,470,471,472,474,477,479,487,490,495],consider:[6,8,239,240,317,318,319,370,478],consist:[3,6,8,9,11,12,40,42,65,69,79,93,105,110,113,114,117,148,151,153,168,180,190,195,200,201,206,220,221,224,226,229,232,239,240,241,252,255,257,258,259,260,261,262,263,264,265,267,268,269,270,272,273,274,275,276,277,278,286,289,294,296,298,299,317,318,319,320,330,355,356,358,364,365,370,372,377,379,385,387,395,398,402,405,416,417,419,422,424,434,437,439,440,452,459,467,469,470,471,472,473,474,481,490,495],consistent_fe_initi:203,consit:299,constant:[],constitu:[3,6,245,299,331,335,385,434],constitut:[437,439],constrain:[3,6,8,145,146,147,148,149,151,154,155,156,157,158,160,161,197,206,221,231,232,237,245,249,284,285,297,299,302,312,322,329,363,364,395,474,481,490],constraint:[],construct:[6,8,12,14,38,54,56,61,64,67,70,72,73,77,92,108,120,142,167,218,255,281,298,335,366,370,390,422,424,449,451,452,472,473,488,495],constructor:[8,11],consult:433,consum:[1,294,428,495],consumpt:353,contact:[],contact_stiff:[436,438],contain:[0,1,2,3,4,6,8,9,11,12,13,17,18,19,38,40,41,56,63,87,91,118,120,142,148,156,166,167,168,170,174,176,187,188,191,193,194,195,197,198,199,203,205,206,207,209,210,211,212,214,219,221,226,233,237,238,239,242,253,269,280,281,284,285,287,289,292,296,299,300,304,314,321,325,326,335,336,339,354,356,364,365,368,369,371,372,373,377,386,387,390,393,394,395,402,403,419,422,426,430,431,432,433,441,451,452,453,454,455,456,458,464,465,466,467,469,470,471,472,474,476,478,481,483,486,487,490,495,497,499],content:[12,18,433,485,487],context:[3,6,8,12,17,118,119,194,215,216,221,284,296,330,362,461,469,476,485,494,495,496],contibut:70,contigu:466,contin:16,continu:[0,2,3,5,6,9,12,13,14,41,71,81,104,105,164,194,197,198,199,204,206,207,208,209,210,211,212,214,217,218,219,220,221,231,232,233,235,236,237,239,240,241,247,252,253,255,257,258,259,260,261,262,263,274,275,276,277,278,283,285,288,289,299,300,303,313,314,316,323,324,326,332,335,339,354,369,370,377,391,392,409,412,432,433,434,437,439,454,464,467,469,471,472,477,483,486,487,495,497],continuum:[6,7,9,203,326,437,439],contour_integr:203,contract:[59,218,220,255,286,299],contradictori:3,contrain:302,contraint:269,contrari:[233,240],contrast:[1,6,42,55,64,150,153,220,337,437,439,461,498],contrib:326,contribut:[3,5,6,7,8,9,12,13,17,63,66,68,70,71,74,75,77,80,84,87,88,89,90,91,94,103,105,107,109,110,111,112,114,116,119,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,199,204,205,206,207,209,210,211,212,218,231,239,242,245,246,250,256,276,277,284,285,293,296,299,300,302,328,355,363,365,373,391,392,393,395,402,416,417,422,424,432,433,440,481,487,490],contributor:12,control:[3,5,6,7,8,9,11,13,16,27,29,41,87,91,124,142,177,191,193,197,203,204,214,218,219,220,235,236,239,240,255,257,258,259,260,261,262,263,286,291,299,305,306,317,318,319,326,330,353,355,367,395,398,422,432,433,436,438,451,455,464,466,478,484,485],control_typ:203,controlfil:433,convect:91,conveni:[6,12,29,191,195,212,300,358,441,495],convent:[3,8,9,29,179,186,187,194,298,311,338,393,395,495],converg:[3,6,41,88,191,193,195,200,214,217,218,226,229,260,289,291,294,298,302,361,362,363,365,386,387,407,440,464,476,483],convers:[3,8,142,193,194,204,207,286,355,387,388,389,395,407,411,415,427,467,483,494],convert:[2,3,4,5,6,7,8,12,13,20,21,24,28,32,35,36,59,63,71,91,168,175,191,193,194,212,253,285,337,340,342,346,349,358,365,371,393,422,453,455,462,467,469,470,471,476,486,490,494,495,497,499],convex:[42,335,376],convinc:[7,12],cook:9,cooki:7,cool:[7,158,235,297],cooordin:191,cooper:[5,7],coord123:116,coord1:[3,116,206,210,211],coord2:[3,116,206,210,211],coord3:[3,116,206,210,211],coord:[],coordb:440,coordbb:440,coordiat:363,coordin:[1,3,4,6,7,8,11,13,14,15,17,40,41,42,59,61,62,63,66,68,71,74,75,77,81,87,89,90,94,104,105,107,115,116,118,136,142,151,157,163,165,166,168,172,190,191,192,193,194,195,197,200,205,206,209,210,211,214,215,216,217,218,219,220,221,224,226,227,229,231,234,235,236,237,238,239,240,252,254,255,257,258,259,261,262,263,276,279,280,281,284,285,286,296,297,299,301,302,303,308,311,312,313,314,316,324,325,326,333,334,336,337,358,363,364,365,370,371,372,375,376,394,440,464,469,470,471,472,474,477,479,483,490,495,496],coordn:[116,206],coorind:[],copi:[0,3,4,8,11,12,15,17,40,121,193,326,365,384,432,467],copper:462,coproccesor:16,coprocessor:[1,4,7,9,16,17,370,482],coproprocessor:17,copy_arrai:8,copyright:[7,8,284],coral:194,core:[],core_shel:150,coreshel:[6,9,380,387,389],cornel:[6,174,481],corner123i:115,corner123x:115,corner123z:115,corner1i:115,corner1x:115,corner1z:115,corner2i:115,corner2x:115,corner2z:115,corner3i:115,corner3x:115,corner3z:115,corner:[3,6,40,115,193,335,336,358,457,469],cornflowerblu:194,cornsilk:194,corpor:16,corr:386,correct:[3,6,9,11,12,16,17,59,87,88,103,104,112,118,150,155,162,193,220,231,233,239,255,256,276,284,286,289,325,331,335,355,365,371,372,373,374,375,376,377,378,379,380,381,382,383,385,386,387,388,389,390,391,392,393,394,395,397,398,399,400,401,402,403,404,405,406,407,408,409,410,411,412,413,414,415,416,417,418,419,420,421,422,423,424,425,427,429,430,431,432,433,434,435,436,437,438,439,440,441,442,443,444,445,446,447,448,449,450,451,452,453,454,455,457,458,460,461,462,469,484,487,490],correction_max_iter:203,correctli:[3,8,9,11,17,71,81,103,104,105,145,146,147,149,151,153,154,155,156,157,160,161,164,191,194,200,221,226,229,240,249,255,256,292,299,302,311,313,332,335,365,366,370,389,417,422,466,467,469,479,494,496],correl:[],correspond:[1,2,6,8,11,12,14,20,21,22,23,24,25,26,27,28,29,30,31,32,35,38,40,42,43,44,45,46,47,48,49,51,53,54,56,70,71,87,97,98,111,114,115,116,117,120,121,129,132,133,134,135,136,138,139,140,142,145,146,155,162,166,167,174,175,176,177,178,179,180,182,183,185,186,188,190,191,193,194,198,199,200,206,208,209,210,211,213,216,218,220,227,229,230,234,239,242,243,251,252,253,255,257,258,259,260,261,262,263,264,265,269,272,274,275,276,278,281,282,286,291,299,301,302,317,319,321,330,331,332,334,335,336,338,340,341,342,343,345,346,349,351,356,360,362,364,365,371,372,374,378,379,380,381,382,383,384,385,386,387,390,391,393,394,395,396,397,398,399,400,401,402,405,407,408,409,410,411,412,413,414,415,416,419,420,422,424,425,426,427,429,430,432,433,434,435,440,441,442,451,452,453,454,455,458,460,461,462,464,466,467,469,470,472,482,483,484,486,487,490,495],correspondingli:[416,417,478],cosin:[],cosineshift:27,cosmo:[233,238],cossq:[],cost:[1,6,10,11,12,17,39,41,71,111,120,143,167,193,194,206,210,211,214,215,216,228,255,291,326,355,356,368,387,407,411,422,424,451,466,478],costheta0:[451,453,455,458],costheta:430,costli:[11,88,233,366],couett:4,coul:[],could:[2,3,6,9,11,12,17,33,41,50,59,66,71,75,87,90,94,105,107,111,114,116,148,158,163,165,181,191,193,194,198,199,206,207,210,214,220,229,238,288,289,290,294,297,299,301,314,315,321,325,326,327,331,335,337,339,347,352,354,361,363,366,370,373,397,401,402,405,432,433,465,466,467,469,471,473,476,477,485,490,495,496],coulomb:[3,5,6,7,8,9,10,12,14,15,18,72,88,109,110,118,143,169,173,290,292,327,355,356,363,370,378,380,381,382,383,386,387,388,389,390,395,399,400,402,407,411,415,418,424,427,432,433,435,440,450,455,456,458,461,474,481,487,490,494],coulommb:6,cound:3,count:[1,3,6,8,10,11,12,16,41,63,68,77,91,116,118,119,156,166,172,200,201,204,206,209,210,211,213,214,221,226,228,231,237,255,269,285,302,317,318,335,356,363,364,365,367,370,397,401,424,487,495],counter:[332,464,475,477,483],counteract:231,counterbal:235,counterbalanc:29,counterpart:[191,299,464],counterproduct:18,coupl:[],courant:304,cours:[3,8,128,130,162,191,198,199,232,298,311,325,331,333,334,336,337,356,416,442,466,469,482,490,495,497],courtesi:358,cov:440,coval:[6,29,395,419,440,490],covari:233,cover:[6,71,188,194,203,242,395,457],coverag:[71,210],cpc:238,cpp:[1,3,6,8,9,11,12,13,87,191,198,199,229,302],cpu:[1,3,4,9,10,12,14,15,16,17,18,63,71,194,208,224,240,327,353,356,370,384,450,464,482,483,486,487,488,495],cpuremain:487,cr2:167,cr3:167,crack:[4,366],crada:[5,7],crai:[5,7,13,18,191],crash:[3,12,366,490],craympi:370,creat:[],create_atom:[],create_bond:[],create_box:[],create_elementset:203,create_faceset:203,create_group:192,create_nodeset:203,createatom:[],creation:[],crimson:194,critchlei:284,criteria:[3,118,169,193,194,215,216,217,250,363,429,457,471,474,495],criterion:[12,41,123,168,171,204,214,217,231,269,291,304,332,337,363,365,386,395,399,440,474,483,484],criterioni:483,critic:[6,48,49,253,321,326,363],crmax:71,crmin:71,cross:[3,12,22,71,89,146,166,176,191,193,205,210,216,220,252,254,276,299,307,311,313,322,329,341,358,365,382,391,392,393,400,401,402,407,409,411,430,435,437,439,453,455,462,469,473,479,497],crossov:1,crossterm:469,crozier:[0,7,13],crucial:289,crystal:[4,6,13,73,108,280,281,324,358,366,473,487,490],crystallin:[6,104,281,358,454,490],crystallis:321,crystallogr:[120,167],crystallograph:[358,487],crystallographi:[120,167,358],cs1:167,cs_chunk:6,cs_im:[40,469],cs_re:[40,469],csanyi:[142,431,441],cscl:419,csequ:6,csh:[11,12,384],cshrc:[11,12],csic:[394,451,453,455,458],csinfo:6,csisi:[394,451,453,455,458],csld:[],cst:393,cstherm:6,cstyle:466,csvr:[],ctcm:[371,393],ctemp_cor:224,cterm:303,ctr:9,ctype:11,cu1:167,cu2:167,cu3au:419,cube:[6,41,166,171,214,224,335,358,490],cubic:[],cuda:[],cuda_arch:15,cuda_get:15,cuda_hom:15,cuda_prec:15,cufft:14,cuh:377,cummul:[3,6,212,215,216,217,219,228,233,239,241,314,317,318,319,320,322,329,401,487],cumul:[6,204,206,209,210,211,225,231,239,253,255,260,269,299,300,365],curli:2,current:[0,1,3,5,6,7,8,9,11,12,13,15,16,17,18,40,41,42,59,61,63,71,73,81,87,103,104,110,118,119,132,143,148,156,158,164,166,169,172,190,191,192,193,194,195,198,199,203,206,210,211,212,214,215,216,217,218,219,220,221,225,226,229,231,233,236,237,239,245,252,255,256,261,262,263,269,274,275,276,278,284,285,290,291,293,296,297,298,299,302,303,304,305,306,307,308,310,312,313,314,317,318,319,325,326,329,330,331,332,333,334,336,337,339,353,354,355,356,359,360,362,363,364,365,370,376,377,384,386,390,393,395,396,399,402,403,406,416,417,419,420,421,424,430,432,433,436,437,438,439,442,453,455,456,459,464,465,466,467,469,470,471,472,473,475,476,477,479,481,483,484,486,487,495,496,497,498,499],curv:[6,168,231,281],curvatur:[398,434,462],custom:[],cut0:467,cut1:478,cut2:478,cut:[],cuthi:[280,292],cutinn:[379,416,417],cutlo:[280,292],cutmax:430,cutoff1:[383,390,407,411,415,418,427,435],cutoff2:[378,380,381,383,389,390,407,411,415,418,427,435],cutoff:[3,6,10,16,18,39,45,46,54,55,61,70,72,73,77,87,92,108,110,117,118,142,166,169,171,172,216,217,222,280,289,290,292,294,296,299,314,327,331,335,337,353,355,356,363,366,367,368,370,371,372,373,374,375,376,377,378,379,380,381,382,383,385,387,388,389,390,391,392,393,394,395,396,397,398,400,401,402,403,405,406,407,408,409,410,411,412,413,414,415,416,417,418,419,420,421,422,423,424,425,426,427,428,429,430,432,433,434,435,440,441,442,443,444,445,447,448,449,450,451,452,453,454,455,456,457,458,459,460,461,462,467,471,474,478,490,495],cutoff_glob:376,cutoff_inn:376,cutoffa:394,cutoffc:394,cuu3:393,cval:167,cvd:321,cvel:303,cvff:[],cwiggl:[3,252,331,334,336,495],cyan:[2,193,194],cycl:[3,231,253,255,256,260],cyclic:[3,188],cygwin:12,cylind:[3,4,71,193,206,237,285,332,335,472],cylindr:[6,237,311,332],cypress:370,cyrot:377,cyrstal:281,d3q15:242,d3q19:242,d_double_doubl:15,d_e:326,d_flag2:288,d_flag:288,d_name:[115,191,288,316,479],d_single_doubl:15,d_single_singl:15,d_sx:288,d_sy:288,d_sz:288,daan:324,dai:12,daili:12,daivi:276,damag:[],dammak:294,damp:[3,6,197,202,239,240,241,246,255,256,260,286,289,290,294,299,317,318,330,332,333,362,363,365,378,380,382,387,390,395,399,407,415,427,435,450,456,483,490],damp_com:240,damp_drud:240,dampen:[299,490],dampflag:[332,399],dan:17,danger:[3,12,231,337,391,487],dangl:171,daniel:9,darden:[356,390],darkblu:194,darkcyan:194,darken:193,darkgoldenrod:194,darkgrai:194,darkgreen:194,darkkhaki:194,darkmagenta:194,darkolivegreen:194,darkorang:194,darkorchid:194,darkr:194,darksalmon:194,darkseagreen:194,darkslateblu:194,darkslategrai:194,darkturquois:194,darkviolet:194,dasgupta:290,dash:[399,486],dat:[6,91,188,203,465],data2xmovi:[],data:[],data_atom:8,data_atom_hybrid:8,data_bodi:8,data_vel:8,data_vel_hybrid:8,databas:[],datafil:[12,13,300],dataset:300,datatyp:3,date:[0,6,12,13,190,432,433,495],datom1:117,datom2:117,datom3:117,datom4:117,datum:[3,6,42,65,68,69,79,93,110,117,191,207],davenport:418,davi:331,david:[9,19,355,356,453,455],daw:[393,430],dbg:14,dcd:[3,6,7,191,192,193,194,195,282,470,474],ddim:190,deactiv:415,dealt:238,debug:[6,7,11,12,13,14,17,120,124,167,168,282,287,353,355,370,403,424,459,467,468,476,479,486,495],deby:[],decai:[92,387,462],decid:[3,6,12,16,71,252,288,299,327,484],decipher:358,declar:192,declin:314,decod:193,decompos:[87,441],decomposit:[3,5,7,18,62,203,282],decoupl:[6,490],decreas:[3,191,200,201,208,217,220,226,229,231,239,325,355],decrement:303,deepli:352,deeppink:194,deepskyblu:194,def:[12,13,467],defaul:61,defect:[6,70,166,422],defgrad:2,defin:[2,3,5,6,7,8,11,12,17,20,21,22,23,24,25,26,27,28,29,30,31,32,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,51,53,54,55,56,57,58,59,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167,168,169,170,171,172,174,175,176,177,178,179,180,182,183,185,186,187,188,189,190,191,192,193,194,197,198,199,200,201,202,203,204,205,206,207,209,210,211,212,213,214,215,216,217,218,220,221,224,225,226,229,230,231,234,237,238,239,240,241,242,250,252,254,255,256,257,258,259,260,261,262,263,265,266,267,270,272,273,274,275,276,277,278,280,281,282,284,285,286,288,290,292,297,299,300,301,302,304,308,312,314,316,317,318,319,320,322,323,324,326,328,329,331,332,333,334,335,336,337,339,340,341,342,343,344,345,346,349,350,351,353,355,356,358,360,362,363,364,365,366,367,368,369,370,372,373,374,375,376,378,379,380,381,382,383,384,385,387,388,390,391,392,394,395,397,398,399,400,401,402,403,405,407,408,409,410,411,412,413,414,415,416,417,418,422,423,424,425,426,427,429,430,432,433,434,435,436,437,438,439,441,442,443,444,445,446,447,448,449,450,451,452,453,454,455,456,457,458,459,460,461,462,463,464,466,467,469,470,472,473,474,475,478,479,480,481,483,484,486,487,490,491,492,493,494,495,496],definit:[2,3,6,8,12,13,78,80,118,142,194,206,207,208,209,210,211,212,220,237,260,300,316,328,331,334,336,338,350,353,364,373,377,385,395,405,430,437,439,441,457,467,469,471,478,480,494,495],defint:487,deform:[],deg2theta:167,deg:490,degener:[3,284],degrad:[8,18,281,356,478],degre:[3,6,8,20,21,24,28,29,32,35,36,38,65,79,92,93,95,97,98,100,102,103,108,114,145,146,147,148,149,150,151,152,153,154,155,156,157,158,160,161,167,168,174,175,178,179,186,188,190,193,206,217,224,231,233,234,239,240,245,255,256,260,261,262,263,274,275,276,278,282,284,298,299,302,317,318,319,324,340,342,346,349,351,363,390,393,401,479,487,490,496],degress:[148,206],del:483,delai:[3,6,12,366,392,487],deleg:402,delet:[2,3,7,8,12,54,57,60,63,166,171,172,197,206,207,209,210,211,212,215,217,228,231,255,300,317,318,337,339,354,364,366,369,424,449,469,470,471,472,480,481,486,491,493,495,496],delete_atom:[],delete_bond:[],delete_el:203,deli:190,delimit:[467,495],deloc:[256,395,440],delr:419,delt_lo:483,delta:[],delta_1:377,delta_3:377,delta_7:377,delta_conf:3,delta_ij:[419,430],delta_mu:3,delta_pi:377,delta_r:430,delta_sigma:377,delta_ua:376,delx:190,delz:190,dem:376,demand:294,demo:11,demon:279,demonstr:[289,419],den:285,dendrim:401,denniston:[9,242,244,245,246,281],denomin:[7,173],denot:[120,224,240,281,292,294,387,400,402,433,437,439],dens:[71,217,395],densiti:[3,6,7,9,18,40,41,59,101,118,128,142,154,166,168,198,199,203,206,210,211,214,220,229,242,245,248,249,281,285,286,290,326,331,358,360,364,371,377,393,419,420,421,430,434,440,444,446,447,448,469,478,479,487,494],density_continu:439,density_summ:439,depart:[0,7],departur:[253,289],depend:[1,2,3,6,8,9,11,12,16,17,18,20,21,22,23,24,25,26,27,28,29,30,31,32,35,38,39,40,41,43,44,45,46,47,48,49,51,53,54,56,61,63,65,68,69,70,71,79,92,93,104,110,111,114,115,116,117,121,142,145,151,155,156,162,168,169,174,175,176,177,178,179,180,182,183,185,186,187,188,190,191,193,194,197,198,199,200,201,204,206,208,209,210,212,213,214,216,218,220,226,227,230,233,234,235,237,239,240,242,244,245,252,255,257,258,259,260,261,262,263,264,265,272,274,275,276,278,280,291,294,296,299,301,302,308,314,317,318,319,321,323,325,326,328,330,331,334,335,336,337,339,340,341,342,343,345,346,349,351,356,358,363,364,366,367,368,370,371,372,374,375,377,378,379,380,381,382,383,384,385,386,387,388,390,391,393,394,395,396,397,398,399,400,401,402,407,408,409,410,411,412,413,414,415,416,419,420,422,423,425,426,427,429,430,432,433,434,435,440,441,442,450,451,452,453,454,455,456,458,460,461,462,464,466,469,471,472,475,479,481,483,486,487,489,495,496],dependend:6,depflag:12,dephas:[464,483],depos:221,deposit:[],deprec:[290,432],depth:[51,146,193,326,398,434],dequidt:9,der:[87,109,385,386,415,432,433,461,490],deriv:[6,7,8,9,38,56,63,87,142,162,188,207,218,220,231,239,252,255,257,258,259,260,261,262,263,280,286,290,294,323,324,326,331,332,335,362,364,372,377,385,390,395,396,400,409,413,414,419,422,432,433,450,452,461,490],derjagin:461,derlet:280,descend:194,descent:[7,362],descib:[40,193,290],describ:[0,1,2,3,4,6,7,8,9,10,11,12,13,14,15,16,17,18,19,38,39,40,41,42,56,62,63,68,70,71,73,88,112,115,118,120,132,142,143,146,147,148,152,153,156,159,161,162,166,167,168,170,171,180,185,188,191,192,197,198,199,206,207,208,209,210,211,212,214,217,218,219,220,221,223,224,232,233,236,237,238,239,240,241,242,244,245,246,250,254,255,256,260,268,277,280,282,287,288,289,290,291,292,299,303,311,314,315,316,317,318,319,320,321,322,323,324,329,331,332,334,339,355,356,358,361,362,363,364,365,369,372,373,375,376,378,379,380,382,383,384,385,386,387,390,393,395,396,398,399,400,402,405,407,408,409,410,411,412,413,414,415,416,417,418,419,422,423,429,430,431,432,433,434,435,440,441,442,449,450,451,452,453,454,455,456,458,460,461,462,464,466,467,469,470,471,472,473,479,482,483,486,495,496,497],descript:[],descriptor:[142,191,403],deserno:356,design:[0,3,6,7,8,9,11,13,14,15,17,120,150,153,167,203,217,223,224,255,256,280,281,300,321,326,373,374,375,376,379,382,387,389,395,415,416,417,420,421,430,433,452,478],desir:[2,3,6,7,11,12,14,15,16,33,40,50,59,71,88,91,114,119,143,150,168,181,190,206,212,218,220,229,231,232,239,240,241,245,255,276,284,285,286,287,290,294,299,302,314,317,318,319,320,325,332,347,352,355,356,358,361,363,364,365,391,393,401,416,417,451,453,455,465,466,467,469,473,478,483,484,486,487,495,496,497],desk:7,desktop:[4,6,7,10,12,193],despit:490,destabil:377,destre:349,destroi:[11,39,215,216],detail:[1,2,3,4,6,7,8,9,11,12,13,14,15,16,17,18,19,22,37,40,41,42,55,63,66,67,68,71,75,78,90,91,94,103,105,107,109,111,113,114,116,119,121,142,143,145,146,147,148,151,161,162,163,165,168,169,172,173,176,187,190,191,193,194,197,198,199,203,206,207,208,209,210,212,214,216,217,218,219,220,221,229,231,232,233,234,236,237,239,241,242,246,252,253,254,255,256,257,258,259,260,261,262,263,267,269,274,275,276,277,278,281,284,285,286,288,289,291,292,293,299,302,314,317,318,319,320,321,322,324,325,326,327,328,329,330,337,339,341,350,355,356,359,363,364,366,367,370,371,372,373,375,376,377,379,381,382,383,384,385,386,387,390,391,395,396,398,399,400,401,402,407,408,409,410,411,412,413,414,415,416,417,418,419,423,424,429,432,433,434,440,441,442,450,457,460,461,467,469,470,471,472,474,475,478,479,481,484,487,488,495,496,499],detect:[2,3,12,42,61,63,86,92,230,285,325,365,386,401,406,464,466,469,480,483,495],determ:370,determin:[1,3,6,8,9,12,15,39,40,42,51,57,58,59,61,62,68,71,87,103,109,111,114,120,121,129,143,156,157,166,167,168,190,191,193,194,195,196,200,201,202,205,206,207,208,209,210,211,212,213,214,218,220,221,224,226,231,234,235,237,239,240,245,250,252,253,255,261,262,263,274,275,276,278,280,282,285,286,289,296,297,298,299,300,301,304,306,308,314,317,318,319,321,327,328,331,332,333,334,335,336,337,350,355,356,358,364,366,367,370,372,373,381,386,390,392,393,397,399,402,403,411,419,422,424,433,434,440,449,452,456,461,466,469,470,472,474,476,479,483,485,486,488,494,495,496],detil:110,devan:[9,435],devanathan:455,develop:[0,3,5,6,7,8,9,11,12,14,15,16,17,18,19,42,236,260,284,289,290,293,372,377,395,421,422,440,458,471],devemi:9,deviat:[253,260,280,397],deviator:9,devic:[1,3,12,15,17,236,370],device_typ:370,devin:[291,386],devis:421,dfactor:193,dff:490,dfft_fftw2:12,dfft_fftw3:12,dfft_fftw:12,dfft_none:12,dfft_singl:[3,12,356],dfft_xxx:12,dfftw:12,dfftw_size:12,dft:[9,293,422],dhi:[59,190,220,285],dhug:[253,289],dhugoniot:[253,289],dia:419,diagnost:[],diagon:[3,6,83,142,143,144,218,255,286,299,329,437,439],diagonalstyl:441,diagram:[41,120,167,187,214,282],diallo:401,diam:[193,194,285,364],diamet:[3,6,40,42,115,168,191,193,194,198,199,239,285,299,314,316,330,332,364,376,385,398,399,409,434,457,461,469,470,479],diamond:[358,395,419],diamter:[40,285],dick:6,dicsuss:252,dictat:[204,253],did:[3,12,363,391,392,393,399,424,453,455,477],didn:3,die:18,diel:[],dielectr:[],diff:[3,6,12,164,328,355],differ:[1,2,3,4,6,7,8,9,10,11,12,14,15,16,17,18,22,37,38,39,41,42,54,55,56,61,64,68,70,71,87,92,95,97,98,122,142,145,146,147,148,149,151,154,155,156,157,158,160,161,162,168,169,171,176,187,188,190,191,193,194,197,199,202,204,206,209,214,215,216,217,218,219,220,224,230,231,232,233,234,235,236,239,240,242,252,255,256,257,258,259,261,262,263,265,267,270,272,273,274,275,278,280,282,284,286,289,290,291,294,297,299,302,303,311,312,314,317,318,319,322,323,324,326,329,330,331,332,335,339,340,350,352,354,355,356,358,359,361,362,364,365,367,368,369,370,371,372,377,381,382,384,385,386,391,393,395,398,399,400,402,405,407,408,410,411,418,419,420,421,423,424,426,430,432,433,434,435,436,437,439,440,441,442,450,451,452,453,455,457,458,461,463,464,466,467,469,471,472,473,474,477,478,479,481,483,484,486,487,488,490,494,495,496,497],differenti:[1,3,6,29,188,355,387,430,454],difficult:[218,282,370,401,478],difficulti:[92,108,302,432],diffract:[],diffus:[],digit:[2,3,194,339,422],dih_table1:188,dih_table2:188,dihedr:[],dihedral_coeff:[],dihedral_cosineshift:27,dihedral_styl:[],dihedralcoeff:3,dihedraltyp:216,dihydrid:395,dij:302,dilat:[],dim1:3,dim2:3,dim:[3,59,71,145,149,150,151,154,155,156,157,158,160,168,190,210,220,237,332,358,419,472,494,495,496],dimdim:495,dimems:281,dimens:[],dimensinon:71,dimension:[3,39,92,114,120,142,145,148,149,150,151,154,155,156,157,158,160,167,189,206,210,254,281,326,358,361,365,430,469,479],dimensionless:[106,123,124,126,129,131,133,138,142,326,356,441,461],dimentionless:137,dimer:[6,299,419],dimgrai:194,dimstr:[41,214],dinola:[286,317],dintel_offload_noaffin:16,dipol:[],dipolar:[4,29,40,191,316,490],dir1:480,dir2:480,dir:[1,3,4,8,9,11,12,253,280,289,313,430,432,433,467,480,495],dirac:142,direc:430,direct:[],directli:[3,6,8,9,11,12,87,115,142,144,191,192,193,200,226,233,237,242,281,300,318,330,332,333,334,335,358,362,370,371,372,378,380,381,387,390,393,395,407,411,424,427,435,449,467,479,480,481,487,495],directoi:14,directori:[0,1,2,3,4,6,7,8,9,11,12,13,14,15,16,17,60,195,219,238,284,290,293,310,314,323,324,365,369,371,372,377,384,386,387,393,394,396,403,404,415,419,420,421,422,426,430,431,432,433,440,441,451,453,454,455,458,467,469,470,471,480,495],disabl:[3,12,16,326,406,467,482,495],disadvantag:[6,214],disallow:[191,220,255],disappear:471,discard:[2,3,41,71,208,210,214,327,335,466,471,472],discontinu:[9,188,363,413],discourag:419,discov:[13,327],discret:[6,8,40,42,193,194,239,242,376],discuss:[],disk:[6,84,85,92,161,189,221,231,285,467],disloc:[70,422],disord:[39,70,422],disp:[],dispar:434,disperion:[390,411],dispers:[3,6,7,9,166,281,355,356,381,390,411,416,424,433,452,458],displac:[],displace_atom:[],displace_box:59,displacemet:472,displai:[11,13,22,37,44,55,176,187,191,193,341,350,384,450],dispters:3,disregard:422,dissip:[6,232,239,281,323,324,379,391,399,416,417,450],dissolut:215,dist:[6,69,91,110,119,191,282,298,392,449,464,496],distanc:[],distinct:[6,224,296,355,434],distinguish:[6,86,142,245,376,395,468],distort:[166,371],distrbut:371,distribut:[],distro:[113,384,429,430],ditto:[8,12,14,15,16,17,18,42,117,216,462,467],div:8,divd:119,diverg:[3,12,39,299,324,471,490,497],divid:[3,6,16,41,91,114,119,128,130,143,165,166,176,187,194,206,207,209,214,220,280,322,329,334,355,363,365,396,433,440,458,478,486,495],divis:[6,242,377,405,415,466,487,495],dl_poli:[6,7],dlambda:162,dlammps_async_imd:236,dlammps_bigbig:[12,39],dlammps_ffmpeg:[3,12,193],dlammps_gzip:[3,12,191,193,325,469,470,474],dlammps_jpeg:[3,12,193],dlammps_longlong_to_long:12,dlammps_memalign:[12,16],dlammps_png:[3,12,193],dlammps_smallbig:12,dlammps_smallsmal:12,dlammps_xdr:[12,191],dlen:479,dlmp_intel_offload:[12,16],dlo:[59,190,220,285],dlopen:6,dlvo:[7,385,461],dm_lb:242,dmax:[314,361],dna:7,doc:[0,1,2,3,4,6,7,8,9,11,12,13,14,15,16,17,18,22,37,40,42,55,57,59,63,66,68,75,87,90,94,103,105,106,107,109,111,113,114,116,119,121,143,146,147,148,161,163,165,168,169,170,176,187,190,191,192,193,194,195,197,198,199,204,205,206,207,208,209,210,211,212,221,231,239,240,250,255,256,261,262,263,267,274,275,276,277,278,285,288,299,311,314,317,318,319,328,332,335,337,339,341,350,354,363,364,365,370,371,372,375,376,384,386,387,393,394,396,401,402,404,405,419,420,421,424,426,429,430,431,441,450,451,453,455,457,458,467,469,470,471,472,474,477,478,479,486,487,495,496,497,498],docuement:434,dodd:[42,376],dodgerblu:194,doe:[0,1,2,3,5,6,7,8,9,11,12,14,15,16,17,18,33,38,39,41,42,50,54,56,59,62,63,67,70,71,72,87,88,91,105,112,118,119,120,144,146,148,150,151,156,158,162,167,168,169,170,172,174,176,181,187,188,190,191,192,193,194,197,203,204,206,210,213,214,216,217,218,220,224,226,228,231,232,235,237,239,240,242,245,251,255,256,257,258,259,261,262,263,274,275,276,277,278,286,287,288,292,294,297,299,314,317,319,321,322,326,329,330,331,334,335,336,337,342,343,344,346,347,349,354,355,356,357,358,364,365,366,371,372,373,374,375,376,377,379,381,382,383,385,386,387,388,390,391,392,393,394,395,397,398,399,400,402,403,404,405,406,409,410,412,413,414,416,417,419,420,421,422,424,430,431,432,433,434,436,437,438,439,440,441,442,443,444,445,446,447,448,449,451,452,453,454,455,456,457,458,460,461,462,464,465,466,467,469,470,471,472,473,476,477,479,480,481,482,483,486,487,490,495,499],doegenomestolif:7,doesn:[3,7,8,12,168,191,204,210,211,311,364,366,370,372,386,394,404,432,433,451,453,454,455,458,469,471],dof:[3,8,114,146,147,148,161,206,299,496],dof_per_atom:[148,206],dof_per_chunk:[148,206],doff:[364,469],doi:[6,219],domain:[3,6,7,12,13,18,39,41,42,58,61,62,71,120,157,167,170,190,192,193,194,197,204,214,218,220,221,235,238,242,255,256,282,294,299,326,331,332,355,356,365,370,392,424,464,466,469,473,486],domin:[1,395,483],don:[0,8,11,12,13,118,171,200,226,240,288,335,419,440,467,469],donadio:318,done:[1,3,6,7,8,12,14,15,16,17,18,38,39,41,56,59,62,71,162,165,168,171,188,191,193,194,203,204,206,208,209,210,211,212,214,215,216,217,218,220,221,229,231,236,237,239,240,247,255,261,262,263,274,275,276,278,279,281,282,283,285,288,296,299,300,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8,209,212,213,214,218,220,221,226,231,232,234,235,237,239,240,242,245,246,252,253,260,271,280,282,285,287,289,290,291,294,296,298,299,301,303,308,310,317,318,319,322,323,324,326,328,329,331,334,336,337,339,354,358,363,365,366,367,369,370,386,391,397,398,401,405,416,422,423,430,432,433,434,436,437,438,440,441,442,452,457,458,462,465,466,467,469,471,472,476,477,480,483,485,487,495,496],equat:[3,6,7,8,9,91,108,114,120,167,176,187,197,218,224,225,233,239,240,242,245,253,254,255,256,260,276,280,282,289,290,294,302,314,322,326,329,331,332,334,336,349,355,356,385,390,391,395,396,399,404,416,417,419,424,434,437,439,444,445,447,448,462,490],equi:256,equidist:254,equil:[3,290,359,476,499],equilater:479,equilibr:[3,4,5,6,7,9,59,91,168,197,204,207,217,218,231,253,255,256,276,277,289,290,291,292,322,323,324,329,386,387,432,433,465,479],equilibria:329,equilibribum:[215,216],equilibrium:[1,3,4,6,7,21,24,26,27,28,29,32,35,36,38,43,47,48,49,51,53,56,59,151,152,175,177,218,220,231,232,233,240,242,255,260,276,289,290,294,298,302,303,311,314,321,322,324,329,340,342,346,349,386,419,426,440,490],equilibrium_angl:8,equilibrium_dist:8,equilibrium_start:203,equival:[6,12,13,29,59,61,126,127,135,140,166,170,194,209,212,218,220,231,239,255,276,286,298,299,334,391,395,440,453,455,469,472,477,478,487,490],equlibrium:6,equliibr:[290,292],er3:167,eradiu:[40,115,395,469],eras:[301,323],erat:[220,417],erc:387,erfc:[387,407,424],erforc:115,erg:494,erhart:[204,393,453,455],ermscal:373,ernst:9,eror:3,eros:419,erose_form:419,erot:[],errata:[453,455],erratum:331,erron:3,error:[],erta:399,ervel:[115,469],escap:[221,490],especi:[8,11,16,156,168,197,204,214,231,289,294,297,298,370,466],espresso:[9,293],essenti:[8,11,12,27,88,130,149,150,151,154,155,156,157,158,160,177,207,260,281,330,356,372,387,407,455,474,487],essex:29,establish:[87,235],estim:[1,3,6,10,12,38,41,56,91,143,203,214,225,253,314,321,355,356,361,424,433,452,483,487],esu:494,esub:419,eta:[6,242,255,289,290,292,330,394,396,398,430,454,458,494],eta_dot:255,eta_ij:430,eta_ji:396,etag:[40,469],etail:487,etap:255,etap_dot:255,etc:[1,2,3,6,7,8,9,10,11,12,13,15,16,39,40,42,54,61,68,89,90,91,95,111,112,115,117,143,145,148,149,150,151,152,154,155,156,157,158,160,162,168,170,171,172,181,191,193,194,197,198,203,204,205,206,209,210,211,212,215,216,220,221,229,231,232,239,255,285,296,300,326,327,335,339,354,355,363,364,365,366,368,393,394,402,415,417,422,428,432,433,451,453,455,458,464,467,469,470,471,476,478,479,483,485,486,487,488,490,494,495,497,499],ethernet:18,etol:[363,365,464,483],etot0:289,etot:[6,95,97,98,112,143,154,194,224,240,253,289,486,487],eu2:167,eu3:167,euler:[363,365],eulerian:203,euqat:443,europhi:242,ev_tal:8,evalu:[2,3,9,11,12,38,56,71,87,88,91,109,119,142,144,148,158,166,168,190,191,193,194,198,199,200,201,203,205,206,207,208,209,210,211,212,213,220,226,232,234,235,237,238,239,240,281,287,290,301,304,308,317,318,319,328,331,334,336,337,339,355,356,361,363,370,422,424,430,436,438,440,452,464,465,467,471,472,474,476,477,478,479,483,485,487,495,496],evalut:[339,467],evan:[156,276],evanseck:[6,20,174,382,481],evapor:[],evaul:[8,363],evdwl:[109,432,433,487],even:[3,6,8,12,15,17,18,34,39,41,52,57,59,61,63,70,71,121,166,169,170,184,188,191,194,197,198,199,204,205,206,209,210,211,212,214,215,216,218,220,221,224,237,240,253,255,256,281,285,294,296,299,300,310,314,322,326,329,331,335,337,348,355,361,363,365,370,375,395,396,399,402,405,424,434,458,459,469,470,472,474,475,476,478,479,481,484,486,487,488,490,499],evenli:[3,41,143,188,214,242,405,459],event:[],eventu:[3,6,12,15,170,290,483],ever:[54,56,238,314],evera:[385,398,434,450],everi:[0,1,2,3,6,8,9,11,12,15,16,39,41,71,72,91,115,121,130,156,171,191,192,193,194,195,197,198,199,200,203,204,205,206,207,208,209,210,211,212,213,214,215,216,217,218,220,221,225,228,229,231,233,235,236,237,242,243,251,255,256,260,279,280,281,285,286,287,288,289,290,291,292,294,296,297,299,300,302,303,314,316,317,318,319,320,321,322,325,326,327,328,329,337,339,354,356,365,366,367,370,391,392,402,415,432,433,440,446,463,464,465,469,471,473,474,476,477,478,483,484,485,487,495,499],everyth:[8,109],everywher:[118,409],eviri:395,evolut:[233,242,282,464],evolv:[242,282,327],ewald:[2,3,5,6,7,8,12,88,112,120,143,327,355,356,363,378,380,381,387,390,395,407,411,427,435,450,452],ewald_disp:390,ewalddisp:3,exact:[22,41,44,71,124,162,171,176,214,217,232,233,239,240,241,285,294,295,314,326,341,355,384,471,476,483,495,497,499],exactli:[3,6,12,14,17,38,41,42,56,59,71,72,91,118,146,152,159,168,188,198,199,209,214,220,225,232,239,240,241,256,268,269,277,281,289,314,319,320,333,370,384,391,393,399,402,416,424,452,471,472,479,483,495],exager:490,examin:[6,8,9,17,217,281],examp:[467,495],exampl:[],exce:[3,6,16,17,18,41,58,71,170,205,206,209,210,211,212,214,218,220,225,228,255,281,296,300,305,306,314,363,370,469,495],exceed:[3,41,59,214,220,255,314,477],excel:395,except:[1,2,5,6,8,9,11,14,20,21,22,23,24,25,26,27,28,29,30,31,32,35,37,38,40,41,43,44,45,46,47,48,49,51,53,54,55,56,59,60,63,71,89,90,110,111,114,119,143,145,146,147,148,149,150,151,152,154,155,156,157,158,159,160,161,168,172,174,175,176,177,178,179,180,182,183,185,186,187,188,190,191,194,197,200,206,207,209,213,214,218,220,227,230,231,234,237,239,241,255,256,257,258,259,260,261,262,263,264,265,268,269,272,274,275,276,277,278,282,291,292,299,301,302,311,314,317,319,320,326,330,334,337,339,340,341,342,343,345,346,349,350,351,355,356,358,360,364,365,366,368,369,370,371,372,374,378,379,380,381,382,383,384,385,386,387,389,390,391,393,394,395,396,397,398,399,400,401,402,407,408,409,410,411,412,413,414,415,416,417,420,425,426,427,429,432,433,434,435,442,450,451,452,453,454,455,458,460,461,462,464,466,467,469,471,472,474,477,478,479,480,481,483,487,490,494,495,496,498],excess:[208,395],exchang:[2,3,6,8,9,61,62,197,203,204,231,239,291,299,322,326,329,355,370,395,484],exchange:355,excit:[9,395],exclud:[3,6,9,12,16,17,63,71,114,142,148,155,156,172,191,206,210,215,216,243,251,284,297,299,321,332,337,363,364,366,379,399,402,405,416,417,424,449,481],exclus:[1,3,9,12,16,87,370,386,422,424,478,488],excurs:[255,464],exectubl:12,execut:[1,2,3,4,6,8,11,12,17,60,169,193,236,293,339,354,357,369,465,467,477,480,483,495],exempl:440,exemplari:232,exemplifi:395,exert:[6,237,240,294,333,334,335,356],exhaust:[203,369,495],exhibit:[92,255,362,395,478],exist:[3,6,7,8,11,12,13,16,37,55,59,68,70,124,168,169,187,192,193,194,197,202,213,216,218,221,231,284,285,287,337,340,342,343,344,346,350,359,364,370,402,432,449,459,465,467,469,470,471,480,481,482,495,496,497],exit:[2,3,11,12,41,57,191,214,354,369,467,468,477,486,495],exlanatori:3,exp:[],expand:[],expans:[12,142,191,480,495],expect:[1,3,8,12,13,14,15,16,17,18,19,41,42,71,103,149,160,166,188,214,226,231,233,252,280,286,288,289,294,299,337,356,366,384,419,422,424,464,467,469,471,474,478,483,495],expens:[6,10,71,194,280,284,299,326,337,355,356,366,370,467],experi:[6,13,15,17,213,221,236,245,254,286,298,299,361,365,391,424,478,483],experienc:[6,12,244,245],experiment:[231,355,370,483],expert:12,expertis:7,explain:[1,3,6,8,9,11,12,16,18,41,59,63,65,68,69,71,72,73,76,77,79,86,93,148,156,188,191,193,194,197,206,207,212,214,216,218,220,255,280,288,299,311,337,339,354,355,358,364,365,369,375,393,405,440,442,457,467,470,471,474,476,479,490,495,499],explan:[3,6,59,115,142,191,206,254,280,402,463,466,467,469,478],explanatori:[3,8,119,191,205,206,209,210,211,299,364,466,495],explantori:[3,295],explic:423,explicit:[6,9,11,22,44,77,87,115,118,162,176,198,199,220,305,306,341,360,372,373,377,382,384,393,395,406,416,456,463,466,470,473],explicitli:[3,6,8,12,14,15,16,17,18,19,20,21,23,24,25,26,27,28,29,30,31,32,35,38,40,43,45,46,47,48,49,51,53,54,56,71,111,114,145,155,158,166,168,174,175,177,178,179,180,182,183,185,186,188,191,194,200,210,213,220,227,230,232,234,239,255,257,258,259,260,261,262,263,264,265,272,274,275,276,278,288,289,291,299,301,302,317,319,320,326,330,334,340,342,343,345,346,349,351,364,370,371,372,374,378,379,380,381,382,383,384,385,386,387,388,390,391,392,393,394,396,397,398,399,400,401,402,406,407,408,409,410,411,412,413,414,415,416,420,422,424,425,426,427,429,434,435,442,443,444,445,446,447,448,450,451,452,453,454,455,456,458,460,461,462,469,471,472,478,479,481,482,488,490],explictli:[16,482],exploit:[9,15,17,282],explor:[120,167],expon:[3,290,292,393,398,401,415,423,435],exponenti:[87,430,451,458,462,483,495],expos:11,exposit:[203,391,392],express:[6,142,154,168,198,199,218,252,280,290,326,332,339,377,393,395,409,419,440,441,450,495],expressiont:377,extend:[],extens:[3,6,9,17,44,45,46,53,55,63,82,83,84,87,88,91,95,98,99,109,111,119,121,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,197,200,201,204,212,213,219,222,226,229,230,231,233,234,235,237,239,241,253,255,260,269,280,281,297,298,299,301,303,308,311,313,317,318,319,320,321,323,324,326,328,331,335,336,398,419,422,433,434,441,486,487],extent:[1,3,41,42,45,57,71,166,170,191,202,210,214,237,333,336,355,358,372,436,438,452,466,469,472],exterior:[3,6,166,335],extern:[],extra:[3,6,8,12,16,17,40,41,46,61,71,103,111,112,114,120,143,145,146,147,149,151,154,155,156,157,158,160,161,167,168,169,170,174,194,209,214,216,255,287,288,289,299,314,363,364,367,368,390,399,402,405,419,424,466,467,469,472,481,490,495],extract:[3,6,11,13,36,63,87,109,117,119,121,198,199,292,365,387,396,419,441,467,474,486],extract_atom:11,extract_comput:[11,467],extract_fix:11,extract_glob:11,extract_vari:11,extramak:[12,15],extrapol:1,extrem:[1,3,6,17,58,193,208,218,220,255,324,395,454,490],extrema:415,extrins:203,f77:[5,7,12],f90:[5,7,12],f_1:6,f_5:[164,328],f_a:[453,454,455],f_ave:119,f_c:454,f_f:455,f_fix_id:289,f_harm:324,f_i:[29,430],f_id:[6,71,119,121,191,197,205,206,207,208,209,210,211,212,250,316,328,487,495],f_ij:430,f_indent:212,f_int:323,f_j:29,f_jj:91,f_k:430,f_langevin:326,f_max:[289,294],f_msst:253,f_r:[240,453,454,455],f_sigma:377,f_solid:324,f_ss:6,f_temp:[],face:[3,6,57,59,71,156,166,170,202,210,211,331,333,334,335,336,358,398,419,434,469,472],face_threshold:166,facet:166,facil:[0,12],facilit:[6,13,42],fact:[6,8,16,233,285,314,324,399,440,481],factor:[1,3,6,12,18,24,28,32,35,36,39,41,46,47,57,58,59,72,87,91,103,110,117,118,120,142,162,167,170,174,185,190,191,193,194,198,199,207,214,218,220,221,231,236,239,241,242,253,255,256,260,282,286,290,298,302,304,306,314,318,322,329,330,331,335,346,356,358,364,370,372,373,377,378,380,382,387,388,389,391,395,399,402,406,407,419,422,424,426,427,433,435,442,451,456,466,469,472,473,478,481,483,484,487,490,494,495],factori:[3,467],factoriz:355,fail:[3,11,12,59,172,218,221,355,363,365,389,433,467],failur:[123,437,468,495],fairli:[11,424,478,483],faken:73,falcon:236,fall:[3,6,194,209,285,467,495],fals:[86,337,339,440,495],fame:8,famili:[458,466],familiar:[0,11],fan:430,far:[3,6,12,17,57,59,61,86,191,194,195,214,215,216,218,221,255,280,298,299,314,331,342,346,361,365,366,457,467,469,474,487],farago:239,farrel:[453,455],farther:191,fashion:[6,8,41,71,168,194,197,198,199,204,210,214,216,221,231,233,237,252,253,255,257,258,259,260,261,262,263,271,274,275,276,277,278,288,289,291,299,303,307,313,316,324,326,330,331,332,334,336,365,402,416,472,481,495,498],fasolino:404,fast:[6,7,9,12,13,17,39,191,266,289,327,355,356,379,416,417,422,450,452,471,476,478,487,496,499],faster:[1,6,9,10,11,12,14,15,17,18,20,21,23,24,25,26,27,28,29,30,31,32,35,38,40,41,43,45,46,47,48,49,51,53,54,56,61,63,106,111,114,145,155,174,175,177,178,179,180,182,183,185,186,188,191,194,200,213,214,220,227,230,234,238,239,255,257,258,259,260,261,262,263,264,265,272,274,275,276,278,286,290,291,299,301,302,314,317,319,321,323,326,330,334,340,342,343,345,346,349,351,355,356,367,368,370,371,372,374,377,378,379,380,381,382,383,384,385,386,387,390,391,393,394,396,397,398,399,400,401,402,407,408,409,410,411,412,413,414,415,416,420,425,426,427,429,434,435,442,450,451,452,453,454,455,458,460,461,462,464,472,478,482,490],fastest:[1,6,14,17,156,210,326,327,370,466],fatal:[3,486],fault:[70,433],faulti:12,fava:398,favor:217,favorit:7,fbmc:321,fcc:[],fcm:[271,495],fdirect:224,fdotr:403,fdti:87,fe2:167,fe3:167,fe_md_boundari:203,featu:8,featur:[],fecr:393,feedback:[7,236],feel:[7,236,237,245,280,335,337,365,424],felling:421,felt:335,femtosecond:494,fene:[],fennel:[387,407],fep:[],ferguson:[6,174,481],fermi:[1,12,15,154,370,455],fermion:[9,395],fernando:418,ferrand:[9,13],few:[1,3,4,5,6,7,9,10,11,12,13,14,18,39,63,195,205,206,207,209,210,211,212,240,255,285,288,290,302,328,355,363,364,365,372,440,466,469,474,478,480,488,495,497],fewer:[1,3,11,15,16,61,245,478],fewest:3,fextern:229,feynman:282,fff:467,ffield:[386,396,432,433,440],ffmpeg:[3,12,193],ffplai:193,fft:[1,3,7,12,14,15,88,111,112,143,281,355,356,478],fft_inc:[12,356],fft_lib:12,fft_path:12,fftbench:[355,488],fftw2:12,fftw3:12,fftw:[11,12],fhg:[7,9],ficiti:449,fictiti:[6,200,201,226,229,233,282,298,387,407,411,449],field1:[470,474],field2:470,field:[],fifth:[311,426],figur:[1,3,8,11,12,289,466,467],fij:390,file0:280,file1:[11,13,280,325,339,364,474,476,480],file2:[11,13,325,339,364,474,476,480],file:[],file_from:192,filen:364,filenam:[3,12,13,38,41,56,188,191,193,194,195,203,206,207,208,209,210,211,212,214,219,280,284,287,290,291,292,295,296,299,300,325,326,352,353,354,364,365,371,372,377,387,393,394,396,404,419,420,421,426,430,431,432,433,440,441,451,452,453,454,455,458,465,466,467,470,471,476,480,487,495,497,498,499],filennam:476,filep:[3,191,194,471,476,499],filepo:296,fill:[7,9,168,193,285,326,358,366,377,422,433,472],filter:[194,203],final_integr:8,final_integrate_respa:8,finchham:[6,150,389],find:[0,3,4,6,7,8,11,12,13,14,16,38,39,56,61,71,73,87,119,171,188,195,204,217,218,228,231,254,280,285,286,294,298,361,363,365,366,387,402,407,411,419,440,450,452,490,495],find_custom:8,fine:[16,17,172,200,226,324,366,370,495],finer:[142,168,495],finest:355,finger:[168,190,252,472],finish:[6,11,41,214,339,352,354,355,367,369,370,457,474,495,496],finit:[],finni:[7,393,450],finvers:224,fiorin:[9,219],fire:[],firebrick:194,first:[0,1,2,3,5,6,8,9,11,12,14,15,16,17,21,38,39,41,42,45,46,54,56,57,59,61,62,71,81,88,91,104,105,106,108,114,118,119,129,132,135,136,140,143,153,156,162,164,166,167,169,170,171,175,188,191,192,193,194,195,197,198,206,207,209,210,211,212,214,217,220,231,232,237,242,252,253,254,255,280,282,287,288,289,291,296,299,302,303,311,312,314,315,316,323,324,325,326,328,332,337,339,340,347,358,363,364,365,366,369,370,371,372,375,377,378,380,382,384,386,387,393,395,396,399,400,402,403,404,405,406,407,411,416,417,419,421,422,424,426,430,432,433,440,441,449,451,452,453,454,455,458,462,464,465,466,467,469,470,471,474,476,478,481,482,483,486,487,490,495,496,497,499],fischer:[6,9,19,20,174,382,481],fit:[3,6,9,12,38,56,188,298,314,372,377,404,419,424,445,452,454,477,495],five:[73,154,289,364,377,420,469,483],fix:[],fix_adapt:[162,199,415],fix_atom_swap:[],fix_bal:62,fix_deposit:[3,204,285],fix_evapor:204,fix_flux:203,fix_gcmc:[204,364],fix_gl:233,fix_gld:233,fix_grav:285,fix_id:[3,218,253,255,257,258,259,260,261,262,263,286,289],fix_modifi:[],fix_mov:[190,332],fix_nh:8,fix_npt:233,fix_nvt:[204,231],fix_poem:[3,6],fix_pour:[3,221],fix_qbmsst:9,fix_qeq:[3,386],fix_rattl:302,fix_reax_bond:432,fix_rigid:[245,375],fix_saed_vtk:300,fix_setforc:8,fix_shak:302,fix_srd:3,fix_styl:260,fix_temp_rescal:320,fixedpoint:[218,255],fixextern:229,fixid:203,fji:390,flag1:[223,368],flag2:[223,368],flag:[3,8,11,12,14,15,16,17,40,66,74,75,81,86,89,90,94,104,105,107,120,163,167,171,191,193,194,195,212,217,219,223,236,239,243,245,251,252,281,288,299,311,313,314,321,325,334,337,353,356,364,368,369,370,372,401,406,419,422,449,464,466,467,469,470,471,473,474,475,479,495],flag_buck:381,flag_coul:[381,390,411],flag_lj:[390,411],flagfld:[379,416,417],flaghi:[3,379,416,417],flaglog:[379,416,417],flagn:223,flagvf:[379,416,417],flat:[6,326,331,332,336],flavor:[2,7,12],fld:[9,331,379,416,417],flen:373,flex_press:373,flexibl:[3,6,8,169,193,206,210,219,233,256,322,329,395,454,487],flip:[3,6,220,255,333,334],floor:495,flop:12,floralwhit:194,flow:[],fluctuat:[6,64,87,218,231,232,239,242,255,260,280,281,324,326,349],fluid:[],fluid_veloc:246,flush:[3,194,486],flux:[],flv:193,fly:[7,9,12,41,193,197,203,208,221,224,299,302,327,377,422,487,490],fmackai:9,fmag:222,fmass:282,fmax:[363,487],fmomentum:224,fmsec:[2,194,239,240,252,255,286,299,317,318,478,489,494,496],fname:354,fno:[12,16],fnorm:[363,487],fnpt:224,fnvt:224,foce:402,fock:373,focu:302,fogarti:[9,292,433],foil:[142,280,441],fold:[312,478],folk:7,follow:[0,1,2,3,4,6,7,8,9,11,12,13,14,15,16,17,18,19,20,23,24,25,26,27,28,29,30,31,32,35,36,38,41,42,43,45,46,47,48,49,51,53,54,56,59,63,64,70,71,73,91,92,97,98,108,115,118,119,121,142,143,146,147,148,154,156,161,164,166,168,169,174,177,178,179,180,182,183,185,186,188,191,192,193,194,197,203,204,205,206,207,208,209,210,211,212,214,219,220,221,224,225,229,231,232,233,236,238,239,240,242,245,253,255,260,261,262,263,274,275,276,278,281,282,284,287,288,289,290,292,294,296,298,299,300,302,316,317,318,319,322,323,324,325,326,328,329,337,338,342,343,344,345,346,349,351,353,358,360,363,364,365,370,371,372,373,374,375,376,377,378,379,380,381,382,383,385,386,387,388,389,390,391,392,393,395,396,397,398,399,400,401,402,403,404,405,406,407,408,409,410,411,412,413,414,415,416,417,418,419,420,421,423,424,425,426,427,429,430,431,432,433,434,435,437,439,440,441,442,443,444,445,446,447,448,449,451,452,453,454,455,456,457,458,460,461,462,464,466,467,469,470,472,474,476,477,478,481,483,484,485,490,495,496,498],foo:[4,8,11,12,191,193,229,467,480,495],foot:6,footprint:[12,370],fopenmp:[12,16,18],forc:[],force_uvm:17,forceatom:245,forcefield:[298,401],forcegroup:242,forcezero:361,ford:390,forestgreen:194,forev:71,forget:[240,490],forgiv:255,fork:[12,191],form:[2,3,6,8,12,19,22,44,54,63,66,74,75,77,81,87,89,90,92,94,104,105,107,118,142,143,162,163,172,176,194,197,198,199,216,232,233,239,241,245,252,276,281,292,294,298,299,326,331,335,340,341,344,349,360,362,364,365,372,373,377,384,393,395,397,401,402,406,418,419,421,422,426,427,430,432,433,434,440,441,442,450,452,453,454,455,461,463,466,467,469,474,479,486,490,495],formal:[6,78,80,91,232,233,239,255,282,314,322,440],format:[2,3,6,7,8,9,12,13,22,38,41,44,56,68,77,176,188,191,192,193,194,195,206,209,210,211,212,214,216,281,284,288,290,292,295,299,300,310,325,326,337,338,341,360,364,365,371,372,377,384,393,396,406,419,421,431,432,433,435,441,452,458,459,466,467,469,470,471,474,485,486,487,495,497],former:[6,12,16,39,41,194,214,326,330,377,379,475,481,495],formerli:[7,13],formul:[1,40,64,143,200,226,239,255,276,290,292,298,302,325,355,372,377,393,395,398,419,429],formula:[2,3,6,7,13,21,22,37,44,54,55,70,73,87,89,90,91,95,97,98,107,114,120,143,145,146,147,148,149,150,151,152,154,155,156,157,158,159,160,161,167,168,173,175,176,187,190,191,198,199,200,201,206,207,208,209,212,213,220,226,234,235,237,239,240,252,280,281,287,296,301,308,312,314,317,318,319,328,331,334,336,337,339,340,341,343,350,358,364,372,373,375,377,382,383,384,385,390,391,393,394,398,399,400,401,403,406,407,409,410,411,413,414,416,417,419,423,424,425,434,435,442,450,451,453,454,455,458,460,461,465,469,472,479,486,487,494,495,496],forth:[1,6,11,12,13,14,15,369,467,472,476],fortran:[3,6,9,11,12,13,229,393,402,419,432,433],fortun:8,forward:[3,8,87,354,365,370],foster:[377,429,430],foul:171,found:[3,6,9,12,73,162,191,217,219,231,236,242,281,321,327,339,354,366,384,387,390,464,470,471,486],four:[6,11,54,81,104,105,142,164,253,326,349,364,365,422,464],fourier:[],fourth:[6,106,298,311,321,382,426,440],fox:[6,120,174,448,481],fphi:[38,56,452],fpic:12,fplo:[38,56,452],fprime:452,fqdn:238,fqq:390,frac:[],fraction:[1,3,6,8,12,16,39,41,80,111,143,171,190,193,194,204,215,216,217,218,253,285,289,296,297,314,319,320,358,365,370,377,379,399,416,417,474,479],fragment:[42,236,296],fraig:[42,376],frame:[83,142,194,203,253,289,333,398],framer:[193,194],framework:[5,233,371,441],franc:9,fraunhof:9,free:[5,6,7,9,13,29,60,63,70,87,162,199,280,314,323,324,325,326,362,365,373,395,415,422,430,461,46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67,495],ilmenau:[7,9,14],ilya:[7,9],imag:[],image2pip:193,imageint:3,imagemagick:[4,193],imagin:[311,325,377,394,402,403,405,420,421,426,430,451,453,454,455,458,481],imaginari:[6,92,231,282,469],imbal:[1,12,41,214,370,488],imbalanc:[41,214],imbu:314,imd:[],img:193,immedi:[0,2,3,8,12,168,215,216,221,302,310,315,316,333,466,467,469,471,483,495,498],immens:3,immers:[242,299],impact:[1,4,6,8,225,321,488],impart:[3,6,234,314,336],impei:[6,407],implement:[1,3,6,8,9,12,17,18,27,78,87,108,120,150,156,167,168,176,177,187,206,219,223,233,236,239,242,244,245,246,253,255,276,279,281,282,288,289,292,293,294,302,303,314,321,326,330,349,354,355,356,363,365,370,371,373,376,377,386,387,389,391,393,394,395,402,407,411,415,419,429,432,433,434,453,455,466,467,478,483,490,495,497],impli:[3,6,40,59,87,143,190,193,198,199,200,220,226,239,298,317,319,320,355,358,384,467],implicit:[],implicitli:8,implict:388,imporop:364,importannt:[],important:324,important_not:[],impos:[2,6,71,114,157,190,197,200,201,213,226,227,229,234,237,246,247,254,269,280,283,301,308,311,313,314,321,322,323,324,329,330,331,334,335,336,363,365,367,463,477],imposs:1,improp:[],improper_coeff:[],improper_styl:[],impropercoeff:3,impropertyp:216,imprort:98,improt:[198,199],improv:[0,1,9,16,39,41,194,214,255,281,370,401,407,422,424,433,451,454],in3:167,inaccur:[1,3,6,171,253,355],inaccuraci:335,inact:401,inappropri:168,incid:[120,167,221],includ:[],includig:[339,354],inclus:[],incom:236,incompat:[3,11,403],incomplet:[3,11,469],incompress:[256,395],inconsist:[3,172,217,470],inconveni:358,incorpor:[289,377,388],incorrect:[3,151,239,419],incorrectli:[3,358,399,495],increas:[1,3,6,10,18,38,56,57,59,111,120,143,188,191,193,194,208,215,216,217,220,231,239,286,297,298,299,322,325,329,355,356,365,370,395,398,433,452,454,467,478,483,495],increasingli:395,increment:[3,11,130,200,201,213,214,221,226,228,255,285,303,304,337,354,369,405,440,464,467,481,483,495],incur:[14,17,206,210,211,228,326,466],inde:151,indefatig:7,indefinit:323,indent:[],independ:[4,6,9,11,12,16,17,41,59,63,91,119,121,154,168,190,197,205,206,207,209,210,211,212,214,217,218,219,220,221,232,234,239,240,242,245,255,281,286,290,294,299,300,303,313,324,326,358,399,422,464,467,486,496],indetermin:[191,194],index:[0,3,6,8,11,12,38,39,40,56,68,69,119,121,166,188,191,194,205,207,236,238,282,300,326,337,338,339,360,369,424,432,433,452,459,469,484,495],indianr:194,indigo:194,indirectli:[6,495],indistinguish:239,indium:441,individu:[],induc:[],industri:7,ineffici:[3,6,40,64,67,70,72,73,77,92,108,142,156,193,220,255,281,355,367],inelig:204,inerti:417,inertia:[],inexpens:[233,478],inf:[2,3,12,329,472],infer:[3,95,97,98,162,200,201,214,215,216,226,236,284,314,322,329,358,384,396,469,481,487],infil:[3,13,299,466],infin:[3,363,474,487],infininti:193,infinit:[3,221,230,237,239,242,281,314,326,332,333,356,358,395,473,494],infinitesim:6,inflect:[388,409],influenc:[3,9,41,80,150,252,285,355,356,424,453,454,455],inform:[0,1,2,3,6,7,8,9,11,12,13,15,17,39,41,42,59,61,62,63,68,88,117,119,120,167,168,174,191,192,193,194,195,197,198,199,200,201,202,203,204,205,206,207,208,209,210,211,212,213,214,215,216,217,218,219,220,221,222,224,225,226,227,228,229,230,231,234,235,236,237,238,239,240,241,242,243,244,245,246,247,248,249,251,254,264,265,266,267,268,269,270,271,272,273,279,280,281,283,284,285,286,287,288,290,291,292,293,294,295,296,297,298,299,300,301,302,304,311,312,314,315,317,318,319,320,321,322,323,325,328,329,330,331,333,334,335,336,338,353,355,356,359,362,363,364,365,366,368,370,371,372,373,374,375,376,377,378,379,380,381,382,383,385,386,387,390,391,392,393,394,395,396,397,398,399,400,401,402,403,404,405,406,407,408,409,410,411,412,413,414,415,416,417,418,419,420,421,422,423,425,427,429,430,431,432,433,434,435,440,441,442,443,444,445,446,447,448,449,450,451,452,453,454,455,457,458,460,461,462,466,467,469,470,471,473,474,476,481,483,484,486,488,495,497,498,499],infrequ:[6,255,391,464,483],infti:[388,416,417],ingtegr:377,inher:[355,363,424],inherit:[6,456],inhomogen:[18,326,424],inidividu:363,init:[3,8,297,440],init_fil:326,init_list:8,init_on:8,init_styl:8,initi:[2,3,4,6,7,8,11,12,13,38,39,40,41,56,57,59,62,71,80,81,86,87,104,105,132,164,169,170,188,190,191,193,194,195,198,199,202,203,207,214,216,217,218,220,227,231,232,236,237,238,239,240,242,247,251,252,253,254,255,260,269,281,282,283,288,289,294,297,298,299,301,313,314,316,321,323,324,325,326,327,328,331,332,333,334,336,337,339,355,359,362,363,365,372,373,376,390,391,392,422,431,432,433,440,452,464,466,467,469,471,472,474,476,477,479,483,484,487,490,495,496,497,499],initial_integr:8,initial_integrate_respa:8,initialis:431,initialt:326,inlclud:11,inlcud:495,inlin:467,inner2:[382,400],inner:[3,8,16,191,237,339,354,361,362,363,365,369,371,372,373,374,375,376,377,378,379,380,381,382,383,385,386,387,388,390,391,392,393,394,395,397,398,399,400,401,402,403,404,405,406,407,408,409,410,411,412,413,414,415,416,417,418,419,420,421,422,423,424,425,427,429,431,432,433,434,435,440,441,442,443,444,445,446,447,448,449,451,452,453,454,455,457,458,459,460,461,462,478,483,495],inner_distance_cutoff:401,innergroup:245,innermost:[38,56,71,368,452,478],innernod:245,innner:413,inordin:327,inorgan:[6,458],inp:[219,339,441,458],input1:[65,68,69,79,93,110,115,116,117,119,121,316],input2:[65,68,69,79,93,110,115,116,117,119,121,316],input:[],input_doubl:3,inquir:304,insensit:12,insert:[3,5,7,8,12,59,168,197,221,231,237,285,355,441,449,467,473,490],insid:[2,3,6,8,11,71,131,137,168,191,194,205,210,211,221,222,228,231,237,242,245,285,299,314,331,333,334,335,336,337,353,358,409,467,468,469,471,472,479,483,495],insight:[6,13],instabl:[242,390,439],instal:[],instanc:[6,11,198,219,233,333,397,402,424,430,467,490],instantan:[6,63,217,218,232,233,255,260,281,286,289,294,296,299,321,475,487],instanti:[6,11,12,203,402,466],instead:[1,3,6,8,9,11,12,13,17,18,40,41,59,61,63,70,71,90,104,119,146,150,172,188,191,199,206,209,210,211,212,214,218,219,231,239,242,245,246,281,287,297,299,316,334,353,355,356,359,366,370,380,381,393,406,408,415,419,422,464,472,476,483,485,490,495],institut:[9,236,284],instruct:[],insuffici:[3,6,12],insult:255,insur:[3,6,11,12,17,39,40,61,73,103,105,168,169,188,191,193,194,200,215,216,221,226,227,228,229,231,234,239,251,287,288,297,299,314,326,331,335,336,337,339,354,364,366,370,385,398,402,428,434,452,466,467,469,470,474,477,478,486,487,495,496],int_max:3,integ:[3,6,8,11,12,39,40,42,64,68,70,71,108,115,117,119,121,142,166,168,171,172,174,178,179,183,188,190,191,193,194,204,206,210,211,215,216,217,221,223,229,231,232,233,236,239,240,241,242,281,284,285,288,289,294,299,314,316,318,321,325,326,345,355,358,379,391,392,405,419,432,433,437,439,441,464,466,467,468,469,477,478,479,483,486,495,496],integr:[],integrate_ulsph:[],intel:[],intel_cpu:[12,16],intel_phi:[12,16],intend:[3,6,8,12,13,36,208,232,431,469],intens:[1,3,6,9,63,66,74,75,86,89,90,91,94,104,105,106,107,114,116,118,119,120,121,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,163,164,165,167,197,206,207,209,210,211,212,214,215,216,217,225,228,235,245,253,255,260,296,299,300,314,322,326,328,329,486,487],intepol:495,inter:[14,18,42,61,62,148,171,172,191,217,239,241,254,291,299,355,365,377,479,490,495,497,499],interact:[1,3,6,7,8,9,10,11,12,14,15,16,17,22,29,33,37,39,40,42,44,50,54,55,57,61,63,65,69,72,77,79,87,88,92,93,108,109,110,112,114,117,118,124,125,126,127,129,130,131,132,133,134,135,137,138,139,140,142,143,144,146,147,161,162,166,169,170,171,172,173,174,176,180,181,187,191,197,198,199,215,216,217,230,231,236,237,239,241,245,269,280,282,284,285,290,292,298,299,305,306,314,315,321,326,330,331,332,335,336,341,342,343,344,346,350,355,356,363,364,365,366,367,368,370,371,372,373,374,375,376,377,378,379,380,381,382,383,384,385,386,387,388,389,390,391,392,393,394,395,396,397,398,399,400,401,402,404,405,406,407,408,409,410,411,412,413,414,415,416,417,418,419,420,421,422,423,424,425,427,429,430,433,434,435,437,439,440,441,442,449,450,451,453,454,455,456,457,458,459,460,461,462,464,467,469,471,473,474,478,479,481,486,487,490,497],interatom:[3,4,7,168,191,254,323,324,371,377,393,395,403,419,422,440,454,495],intercept:120,interchang:6,interconnect:18,interconvert:395,intereract:39,interesect:335,interest:[1,5,7,8,9,11,13,71,167,282,321,324,356,394,417,432,433,467,495],interf:370,interfac:[],interfer:[12,255,372],interg:[6,490],intergr:[478,482],interi:417,interior:[3,6,41,335,472],interlac:419,interleav:[6,168,477],intermedi:[6,12,59,193,254,280,349,365,467,468,477,481],intermix:464,intermolecular:372,intern:[0,2,3,5,6,9,11,16,20,21,24,28,32,35,36,39,40,42,63,87,100,102,120,143,148,150,167,175,188,193,194,197,198,199,203,216,220,224,236,248,249,253,255,260,281,285,299,303,340,342,346,349,353,363,364,443,444,452,467,469,471,474,483,486,487,494,495,496,497],internal_element_set:203,internal_quadratur:203,internet:238,interpenetr:419,interpentr:[444,445,447],interpol:[6,15,38,56,101,188,193,194,203,242,280,355,356,365,377,424,433,446,452,453],interpret:[2,6,11,193,209,399,442,464,467,483,495],interrupt:289,intersect:[3,6,120,194,335,337,472],intersert:335,interspers:363,interstiti:[166,422],intertia:[3,94],interv:[3,6,91,192,207,239,255,289,294,295,306,440,446,464,483,495],intestieti:120,intial:[6,370,372],intiial:[41,474],intiti:[3,313],intra:299,intra_energi:231,intramolecular:[29,231],introduc:[6,9,92,108,193,255,289,294,299,349,355,371,387,395,407,411,415,451,483,495],introduct:[],intsal:[],intuit:358,inv:[120,167,300],invalid:[3,12,71,89,171,269,365,416,417,471],invari:[108,135,140,142],invent:302,invers:[],invert:[1,6,172,281],invis:335,invoc:[166,217,370,437,439,467],invok:[1,3,6,7,8,11,12,13,14,16,17,18,20,21,23,24,25,26,27,28,29,30,31,32,35,38,40,41,43,45,46,47,48,49,51,53,54,56,59,63,66,71,74,75,81,87,88,89,90,94,104,105,107,111,112,113,114,119,145,155,162,163,166,168,169,171,172,174,175,177,178,179,180,182,183,185,186,188,191,193,194,195,197,198,199,200,201,202,203,204,205,206,207,208,209,210,211,212,213,214,215,216,217,2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Documentation","5. Accelerating LAMMPS performance","3. Commands","12. Errors","7. Example problems","13. Future and history","6. How-to discussions","1. Introduction","10. Modifying & extending LAMMPS","4. Packages","8. Performance & scalability","11. Python interface to LAMMPS","2. Getting Started","9. Additional tools","5.USER-CUDA package","5.GPU package","5.USER-INTEL package","5.KOKKOS package","5.USER-OMP package","5.OPT package","angle_style charmm command","angle_style class2 command","angle_coeff command","angle_style cosine command","angle_style cosine/delta command","angle_style cosine/periodic command","angle_style cosine/shift command","angle_style cosine/shift/exp command","angle_style cosine/squared command","angle_style dipole command","angle_style fourier command","angle_style fourier/simple command","angle_style harmonic command","angle_style hybrid command","angle_style none command","angle_style quartic command","angle_style sdk command","angle_style command","angle_style table command","atom_modify command","atom_style command","balance command","Body particles","bond_style class2 command","bond_coeff command","bond_style fene command","bond_style fene/expand command","bond_style harmonic command","bond_style harmonic/shift command","bond_style harmonic/shift/cut command","bond_style hybrid command","bond_style morse command","bond_style none command","bond_style nonlinear command","bond_style quartic command","bond_style command","bond_style table command","boundary command","box command","change_box command","clear command","comm_modify command","comm_style command","compute command","compute ackland/atom command","compute angle/local command","compute angmom/chunk command","compute basal/atom command","compute body/local command","compute bond/local command","compute centro/atom command","compute chunk/atom command","compute cluster/atom command","compute cna/atom command","compute com command","compute com/chunk command","compute contact/atom command","compute coord/atom command","compute damage/atom command","compute dihedral/local command","compute dilatation/atom command","compute displace/atom command","compute erotate/asphere command","compute erotate/rigid command","compute erotate/sphere command","compute erotate/sphere/atom command","compute event/displace command","compute fep command","compute group/group command","compute gyration command","compute gyration/chunk command","compute heat/flux command","compute hexorder/atom command","compute improper/local command","compute inertia/chunk command","compute ke command","compute ke/atom command","compute ke/atom/eff command","compute ke/eff command","compute ke/rigid command","compute meso/e/atom command","compute meso/rho/atom command","compute meso/t/atom command","compute_modify command","compute msd command","compute msd/chunk command","compute msd/nongauss command","compute omega/chunk command","compute orientorder/atom command","compute pair command","compute pair/local command","compute pe command","compute pe/atom command","compute plasticity/atom command","compute pressure command","compute property/atom command","compute property/chunk command","compute property/local command","compute rdf command","compute reduce command","compute saed command","compute slice command","compute smd/contact_radius command","compute smd/damage command","compute smd/hourglass_error command","compute smd/internal_energy command","compute smd/plastic_strain command","compute smd/plastic_strain_rate command","compute smd/rho command","compute smd/tlsph_defgrad command","compute smd/tlsph_dt command","compute smd/tlsph_num_neighs command","compute smd/tlsph_shape command","compute smd/tlsph_strain command","compute smd/tlsph_strain_rate command","compute smd/tlsph_stress command","compute smd/triangle_mesh_vertices","compute smd/ulsph_num_neighs command","compute smd/ulsph_strain command","compute smd/ulsph_strain_rate command","compute smd/ulsph_stress command","compute smd/vol command","compute sna/atom command","compute stress/atom command","compute force/tally command","compute temp command","compute temp/asphere command","compute temp/body command","compute temp/chunk command","compute temp/com command","compute temp/cs command","compute temp/deform command","compute temp/deform/eff command","compute temp/drude command","compute temp/eff command","compute temp/partial command","compute temp/profile command","compute temp/ramp command","compute temp/region command","compute temp/region/eff command","compute temp/rotate command","compute temp/sphere command","compute ti command","compute torque/chunk command","compute vacf command","compute vcm/chunk command","compute voronoi/atom command","compute xrd command","create_atoms command","create_bonds command","create_box command","delete_atoms command","delete_bonds command","dielectric command","dihedral_style charmm command","dihedral_style class2 command","dihedral_coeff command","dihedral_style cosine/shift/exp command","dihedral_style fourier command","dihedral_style harmonic command","dihedral_style helix command","dihedral_style hybrid command","dihedral_style multi/harmonic command","dihedral_style nharmonic command","dihedral_style none command","dihedral_style opls command","dihedral_style quadratic command","dihedral_style command","dihedral_style table command","dimension command","displace_atoms command","dump command","dump h5md command","dump image command","dump_modify command","dump molfile command","echo command","fix command","fix adapt command","fix adapt/fep command","fix addforce command","fix addtorque command","fix append/atoms command","fix atc command","fix atom/swap command","fix ave/atom command","fix ave/chunk command","fix ave/correlate command","fix ave/correlate/long command","fix ave/histo command","fix ave/spatial command","fix ave/spatial/sphere command","fix ave/time command","fix aveforce command","fix balance command","fix bond/break command","fix bond/create command","fix bond/swap command","fix box/relax command","fix colvars command","fix deform command","fix deposit command","fix drag command","fix drude command","fix drude/transform/direct command","fix dt/reset command","fix efield command","fix enforce2d command","fix evaporate command","fix external command","fix freeze command","fix gcmc command","fix gld command","fix gle command","fix gravity command","fix heat command","fix imd command","fix indent command","fix ipi command","fix langevin command","fix langevin/drude command","fix langevin/eff command","fix lb/fluid command","fix lb/momentum command","fix lb/pc command","fix lb/rigid/pc/sphere command","fix lb/viscous command","fix lineforce command","fix meso command","fix meso/stationary command","fix_modify command","fix momentum command","fix move command","fix msst command","fix neb command","fix nvt command","fix nvt/eff command","fix nph/asphere command","fix nph/body command","fix nph/sphere command","fix nphug command","fix npt/asphere command","fix npt/body command","fix npt/sphere command","fix nve command","fix nve/asphere command","fix nve/asphere/noforce command","fix nve/body command","fix nve/eff command","fix nve/limit command","fix nve/line command","fix nve/noforce command","fix nve/sphere command","fix nve/tri command","fix nvt/asphere command","fix nvt/body command","fix nvt/sllod command","fix nvt/sllod/eff command","fix nvt/sphere command","fix oneway command","fix orient/fcc command","fix phonon command","fix pimd command","fix planeforce command","fix poems","fix pour command","fix press/berendsen command","fix print command","fix property/atom command","fix qbmsst command","fix qeq/point command","fix qeq/comb command","fix qeq/reax command","fix qmmm command","fix qtb command","fix reax/bonds command","fix reax/c/species command","fix recenter command","fix restrain command","fix rigid command","fix saed/vtk command","fix setforce command","fix shake command","fix smd command","fix smd/adjust_dt command","fix smd/integrate_tlsph command","fix smd/integrate_ulsph command","fix smd/move_tri_surf command","fix smd/setvel command","<no title>","fix smd/wall_surface command","fix spring command","fix spring/rg command","fix spring/self command","fix srd command","fix store/force command","fix store/state command","fix temp/berendsen command","fix temp/csvr command","fix temp/rescale command","fix temp/rescale/eff command","fix tfmc command","fix thermal/conductivity command","fix ti/rs command","fix ti/spring command","fix tmd command","fix ttm command","fix tune/kspace command","fix vector command","fix viscosity command","fix viscous command","fix wall/lj93 command","fix wall/gran command","fix wall/piston command","fix wall/reflect command","fix wall/region command","fix wall/srd command","group command","group2ndx command","if command","improper_style class2 command","improper_coeff command","improper_style cossq command","improper_style cvff command","improper_style distance command","improper_style fourier command","improper_style harmonic command","improper_style hybrid command","improper_style none command","improper_style ring command","improper_style command","improper_style umbrella command","include command","info command","jump command","kspace_modify command","kspace_style command","label command","lattice command","log command","mass command","min_modify command","min_style command","minimize command","molecule command","neb command","neigh_modify command","neighbor command","newton command","next command","package command","pair_style adp command","pair_style airebo command","pair_style awpmd/cut command","pair_style beck command","pair_style body command","pair_style body/rounded/polygon command","pair_style bop command","pair_style born command","pair_style brownian command","pair_style buck command","pair_style buck/long/coul/long command","pair_style lj/charmm/coul/charmm command","pair_style lj/class2 command","pair_coeff command","pair_style colloid command","pair_style comb command","pair_style coul/cut command","pair_style coul/diel command","pair_style born/coul/long/cs command","pair_style lj/cut/dipole/cut command","pair_style dpd command","pair_style dsmc command","pair_style eam command","pair_style edip command","pair_style eff/cut command","pair_style eim command","pair_style gauss command","pair_style gayberne command","pair_style gran/hooke command","pair_style lj/gromacs command","pair_style hbond/dreiding/lj command","pair_style hybrid command","pair_style kim command","pair_style lcbop command","pair_style line/lj command","pair_style list command","pair_style lj/cut command","pair_style lj96/cut command","pair_style lj/cubic command","pair_style lj/expand command","pair_style lj/long/coul/long command","pair_style lj/sf command","pair_style lj/smooth command","pair_style lj/smooth/linear command","pair_style lj/cut/soft command","pair_style lubricate command","pair_style lubricateU command","pair_style lj/mdf command","pair_style meam command","pair_style meam/spline","pair_style meam/sw/spline","pair_style mgpt command","pair_style mie/cut command","pair_modify command","pair_style morse command","pair_style nb3b/harmonic command","pair_style nm/cut command","pair_style none command","pair_style peri/pmb command","pair_style polymorphic command","pair_style quip command","pair_style reax command","pair_style reax/c command","pair_style resquared command","pair_style lj/sdk command","pair_style smd/hertz command","pair_style smd/tlsph command","pair_style smd/tri_surface command","pair_style smd/ulsph command","pair_style smtbq command","pair_style snap command","pair_style soft command","pair_style sph/heatconduction command","pair_style sph/idealgas command","pair_style sph/lj command","pair_style sph/rhosum command","pair_style sph/taitwater command","pair_style sph/taitwater/morris command","pair_style srp command","pair_style command","pair_style sw command","pair_style table command","pair_style tersoff command","pair_style tersoff/mod command","pair_style tersoff/zbl command","pair_style thole command","pair_style tri/lj command","pair_style vashishta command","pair_write command","pair_style yukawa command","pair_style yukawa/colloid command","pair_style zbl command","partition command","prd command","print command","processors command","python command","quit command","read_data command","read_dump command","read_restart command","region command","replicate command","rerun command","reset_timestep command","restart command","run command","run_style command","set command","shell command","special_bonds command","suffix command","tad command","temper command","thermo command","thermo_modify command","thermo_style command","timer command","timestep command","<no title>","uncompute command","undump command","unfix command","units command","variable command","velocity command","write_data command","write_dump command","write_restart command"],titleterms:{"break":215,"default":[37,39,40,55,57,58,59,61,62,71,87,88,92,103,104,106,108,109,120,124,125,142,148,156,157,161,167,168,171,173,187,189,190,191,193,194,195,196,198,199,200,202,203,204,206,210,211,212,215,216,218,219,220,221,225,228,231,232,237,239,240,241,242,243,245,250,253,255,256,260,276,277,281,282,285,286,287,288,289,291,294,296,297,299,300,314,316,321,322,323,324,327,329,331,333,337,350,353,355,356,358,359,361,362,364,366,367,368,370,373,377,379,395,416,417,422,424,432,433,449,450,464,465,466,469,470,472,474,476,477,478,481,483,485,486,487,488,489,494,496,497,498],"function":495,"long":[208,378,380,381,382,383,387,389,390,407,411,415,427,435],"new":8,"static":12,acceler:1,ackland:64,acknowledg:7,adapt:[198,199],addforc:200,addit:[12,13],addtorqu:201,adiabat:6,adjust_dt:304,adp:371,airebo:372,alloi:393,amber2lmp:13,amber:6,angl:[8,65],angle_coeff:22,angle_styl:[2,20,21,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38],angmom:66,append:202,arrai:6,aspher:[6,82,146,257,261,265,266,274],atc:[9,203],atom:[6,7,8,64,67,70,71,72,73,76,77,78,80,81,85,92,96,97,100,101,102,108,112,113,115,142,143,166,202,204,205,288,495],atom_modifi:39,atom_styl:40,attract:5,aug:[],aveforc:213,awpmd:[9,373],balanc:[41,214],barostat:6,basal:67,beck:374,berendsen:[286,317],between:6,binary2txt:13,bodi:[6,8,42,68,147,258,262,267,275,375,376],bond:[8,13,69,215,216,217,295],bond_coeff:44,bond_styl:[2,43,45,46,47,48,49,50,51,52,53,54,55,56],bop:377,born:[378,389],boundari:[7,57],box:[6,58,218],brownian:379,buck:[380,381,389,418],bug:3,build:[9,11,12],calcul:6,call:12,categori:2,centro:70,ch2lmp:13,chain:13,change_box:59,charmm:[6,20,174,382,415],chunk:[6,66,71,75,90,94,105,107,116,148,163,165,206],citat:7,class2:[21,43,175,340,383],clear:60,cluster:72,cmm:9,cna:73,code:6,coeffici:6,colloid:[331,385,461],colvar:[9,13,219],com:[74,75,149],comb3:386,comb:[291,386],come:5,comm_modifi:61,comm_styl:62,comman:[],command:[2,6,8,12,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167,168,169,170,171,172,173,174,175,176,177,178,179,180,181,182,183,184,185,186,187,188,189,190,191,192,193,194,195,196,197,198,199,200,201,202,203,204,205,206,207,208,209,210,211,212,213,214,215,216,217,218,219,220,221,222,223,224,225,226,227,228,229,230,231,232,233,234,235,236,237,238,239,240,241,242,243,244,245,246,247,248,249,250,251,252,253,254,255,256,257,258,259,260,261,262,263,264,265,266,267,268,269,270,271,272,273,274,275,276,277,278,279,280,281,282,283,284,285,286,287,288,289,290,291,292,293,294,295,296,297,298,299,300,301,302,303,304,305,306,307,308,310,311,312,313,314,315,316,317,318,319,320,321,322,323,324,325,326,327,328,329,330,331,332,333,334,335,336,337,338,339,340,341,342,343,344,345,346,347,348,349,350,351,352,353,354,355,356,357,358,359,360,361,362,363,364,365,366,367,368,369,370,371,372,373,374,375,376,377,378,379,380,381,382,383,384,385,386,387,388,389,390,391,392,393,394,395,396,397,398,399,400,401,402,403,404,405,406,407,408,409,410,411,412,413,414,415,416,417,418,419,420,421,422,423,424,425,426,427,428,429,430,431,432,433,434,435,436,437,438,439,440,441,442,443,444,445,446,447,448,449,450,451,452,453,454,455,456,457,458,459,460,461,462,463,464,465,466,467,468,469,470,471,472,473,474,475,476,477,478,479,480,481,482,483,484,485,486,487,488,489,491,492,493,494,495,496,497,498,499],common:3,comparison:1,compos:6,compress:9,comput:[2,6,8,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167,495],compute_modifi:103,condit:7,conduct:[6,322],constant:6,constraint:7,contact:76,contact_radiu:122,coord:77,core:6,correl:[207,208],cosin:[23,24,25,26,27,28,177],cossq:342,coul:[378,380,381,382,383,387,388,389,400,407,411,415,427,435],coupl:6,creat:216,create_atom:168,create_bond:169,create_box:170,createatom:13,creation:7,csld:318,csvr:318,cubic:409,cuda:[9,14,111,114,145,155,200,213,227,230,234,255,264,301,302,317,319,330,378,380,382,383,393,399,400,407,408,410,413,425,451,453],custom:8,cut:[49,373,380,383,387,390,395,397,407,408,415,423,427],cvff:343,damag:[78,123],data2xmovi:13,data:6,databas:13,deby:[387,407],dec:[],deform:[151,152,220],delete_atom:171,delete_bond:172,delta:24,deposit:221,descript:[20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167,168,169,170,171,172,173,174,175,176,177,178,179,180,181,182,183,184,185,186,187,188,189,190,191,192,193,194,195,196,197,198,199,200,201,202,203,204,205,206,207,208,209,210,211,212,213,214,215,216,217,218,219,220,221,222,223,224,225,226,227,228,229,230,231,232,233,234,235,236,237,238,239,240,241,242,243,244,245,246,247,248,249,250,251,252,253,254,255,256,257,258,259,260,261,262,263,264,265,266,267,268,269,270,271,272,273,274,275,276,277,278,279,280,281,282,283,284,285,286,287,288,289,290,291,292,293,294,295,296,297,298,299,300,301,302,303,304,305,306,307,308,310,311,312,313,314,315,316,317,318,319,320,321,322,323,324,325,326,327,328,329,330,331,332,333,334,335,336,337,338,339,340,341,342,343,344,345,346,347,348,349,350,351,352,353,354,355,356,357,358,359,360,361,362,363,364,365,366,367,368,369,370,371,372,373,374,375,376,377,378,379,380,381,382,383,384,385,386,387,388,389,390,391,392,393,394,395,396,397,398,399,400,401,402,403,404,405,406,407,408,409,410,411,412,413,414,415,416,417,418,419,420,421,422,423,424,425,426,427,428,429,430,431,432,433,434,435,436,437,438,439,440,441,442,443,444,445,446,447,448,449,450,451,452,453,454,455,456,457,458,459,460,461,462,463,464,465,466,467,468,469,470,471,472,473,474,475,476,477,478,479,480,481,482,483,484,485,486,487,488,489,491,492,493,494,495,496,497,498,499],diagnost:7,diel:388,dielectr:173,diffract:9,diffus:6,dihedr:[8,79],dihedral_coeff:176,dihedral_styl:[2,174,175,177,178,179,180,181,182,183,184,185,186,187,188],dilat:80,dimens:189,dipol:[6,29,390],direct:224,discuss:6,disp:6,displac:[81,86],displace_atom:190,distanc:344,distribut:[7,12],document:0,dpd:391,drag:222,dreid:[6,401],drude:[6,9,153,223,224,240],dsf:[387,407],dsmc:392,dump:[6,8,191,192,193,195],dump_modifi:194,dynam:290,eam:[13,393],echo:196,edip:394,eff:[9,13,97,98,152,154,159,241,256,268,277,320,395],efield:226,eim:396,elast:6,emac:13,enforce2d:227,ensembl:7,erot:[82,83,84,85],error:3,evapor:228,event:86,exampl:[1,4,6,11,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167,168,169,170,171,172,173,174,175,176,177,178,179,180,181,182,183,184,185,186,187,188,189,190,191,192,193,194,195,196,197,198,199,200,201,202,203,204,205,206,207,208,209,210,211,212,213,214,215,216,217,218,219,220,221,222,223,224,225,226,227,228,229,230,231,232,233,234,235,236,237,238,239,240,241,242,243,244,245,246,247,248,249,250,251,252,253,254,255,256,257,258,259,260,261,262,263,264,265,266,267,268,269,270,271,272,273,274,275,276,277,278,279,280,281,282,283,284,285,286,287,288,289,290,291,292,293,294,295,296,297,298,299,300,301,302,303,304,305,306,307,308,310,311,312,313,314,315,316,317,318,319,320,321,322,325,326,327,328,329,330,331,332,333,334,335,336,337,338,339,340,341,342,343,344,345,346,347,348,349,350,351,352,353,354,355,356,357,358,359,360,361,362,363,364,365,366,367,368,369,370,371,372,373,374,375,376,377,378,379,380,381,382,383,384,385,386,387,388,389,390,391,392,393,394,395,396,397,398,399,400,401,402,403,404,405,406,407,408,409,410,411,412,413,414,415,418,419,420,421,422,423,424,425,426,427,428,429,430,431,432,433,434,435,436,437,438,439,440,441,442,443,444,445,446,447,448,449,450,451,452,453,454,455,456,457,458,459,460,461,462,463,464,465,466,467,468,469,470,471,472,473,474,475,476,477,478,479,480,482,483,484,485,486,487,488,489,491,492,493,494,495,496,497,498,499],exp:[27,177],expand:[46,410],extend:[8,11],extern:229,fcc:280,featur:[7,8,495],fene:[45,46],fep:[9,13,87,199],field:[6,7],file:6,finit:6,fire:290,fix:[2,6,8,197,198,199,200,201,202,203,204,205,206,207,208,209,210,211,212,213,214,215,216,217,218,219,220,221,222,223,224,225,226,227,228,229,230,231,232,233,234,235,236,237,238,239,240,241,242,243,244,245,246,247,248,249,251,252,253,254,255,256,257,258,259,260,261,262,263,264,265,266,267,268,269,270,271,272,273,274,275,276,277,278,279,280,281,282,283,284,285,286,287,288,289,290,291,292,293,294,295,296,297,298,299,300,301,302,303,304,305,306,307,308,310,311,312,313,314,315,316,317,318,319,320,321,322,323,324,325,326,327,328,329,330,331,332,333,334,335,336,495],fix_modifi:[198,199,200,201,202,203,204,205,206,207,208,209,210,211,212,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7,18,19,370],pair:[6,109,110],pair_coeff:384,pair_modifi:424,pair_styl:[2,371,372,373,374,375,376,377,378,379,380,381,382,383,385,386,387,388,389,390,391,392,393,394,395,396,397,398,399,400,401,402,403,404,405,406,407,408,409,410,411,412,413,414,415,416,417,418,419,420,421,422,423,425,426,427,428,429,430,431,432,433,434,435,436,437,438,439,440,441,442,443,444,445,446,447,448,449,450,451,452,453,454,455,456,457,458,460,461,462],pair_writ:459,pairwis:8,parallel:11,paramet:6,pars:2,partial:155,particl:[6,7,42],partit:463,past:5,per:6,perform:[1,10],peri:429,period:25,phonon:[9,13,281],pimd:282,piston:333,planeforc:283,plastic:113,plastic_strain:126,plastic_strain_r:127,pmb:429,poem:[9,284],point:290,polariz:6,poli:[379,416,417],polygon:376,polym:13,polymorph:430,post:7,potenti:[2,6,8],pour:285,pppm:6,prd:464,pre:7,press:286,pressur:114,previou:12,print:[287,465],problem:[3,4],process:[6,7],processor:466,profil:156,properti:[6,115,116,117,288],pymol_aspher:13,python:[9,11,13,467],qbmsst:289,qeq:[290,291,292],qmmm:[9,293],qtb:[9,294],quadrat:186,quantiti:6,quartic:[35,54],quip:431,quit:468,ramp:157,rattl:302,rdf:118,read_data:469,read_dump:470,read_restart:471,reax:[9,13,292,295,296,432,433],reaxc:9,rebo:372,recent:297,reduc:119,refer:495,reflect:334,region:[8,119,158,159,335,472,495],relat:[20,21,22,23,24,25,26,27,28,29,30,31,32,33,35,36,37,38,40,41,43,44,45,46,47,48,49,50,51,53,54,55,56,57,59,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,83,84,85,86,87,89,91,92,93,94,95,96,97,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,166,167,168,169,170,171,172,173,174,175,176,177,178,179,180,181,182,183,185,186,187,188,189,190,191,192,193,194,195,197,198,199,200,201,202,203,204,205,206,207,208,209,210,211,212,213,214,215,216,217,218,219,220,221,222,223,224,225,226,228,230,231,232,233,234,235,238,239,240,241,242,243,244,245,246,247,248,249,250,251,252,253,254,255,256,257,258,259,260,261,262,263,264,265,266,267,268,269,270,271,272,273,274,275,276,277,278,279,280,281,283,284,285,286,287,288,289,290,291,292,294,295,296,297,299,300,301,303,304,305,306,307,310,311,312,313,314,315,316,317,318,319,320,321,322,323,324,326,327,328,329,330,331,332,333,334,335,336,337,338,339,340,341,342,343,344,345,346,347,349,350,351,352,353,354,355,356,358,361,362,363,364,365,366,367,368,369,370,371,372,373,374,375,376,377,378,379,380,381,382,383,384,385,386,387,388,389,390,391,392,393,394,395,396,397,398,399,400,401,402,403,404,405,406,407,408,409,410,411,412,413,414,415,416,417,418,419,420,421,422,423,424,425,426,427,429,430,431,432,433,434,435,436,437,438,439,441,442,443,444,445,446,447,448,449,450,451,452,453,454,455,456,457,458,459,460,461,462,463,464,465,466,467,468,469,470,471,472,474,475,476,477,478,479,481,482,483,484,485,486,487,488,489,491,492,493,495,496,497,498,499],relax:218,replic:473,replica:[6,7],report:3,requir:12,rerun:474,rescal:[319,320],reset:225,reset_timestep:475,resquar:434,restart2data:13,restart:[6,198,199,200,201,202,203,204,205,206,207,208,209,210,211,212,213,214,215,216,218,219,220,221,222,224,225,226,227,228,229,230,231,233,234,235,236,237,238,239,240,241,242,243,244,245,246,247,248,249,251,252,253,254,255,256,257,258,259,260,261,262,263,264,265,266,267,268,269,270,271,272,273,274,275,276,277,278,279,280,281,283,284,285,286,287,288,289,290,291,292,293,295,296,297,298,299,300,301,302,303,304,305,306,307,308,310,311,312,313,314,315,316,317,318,319,320,321,322,323,324,325,326,328,329,330,331,332,333,334,335,336,476],restrain:298,restrict:[14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167,168,169,170,171,172,173,174,175,176,177,178,179,180,181,182,183,184,185,186,187,188,189,190,191,192,193,194,195,196,197,198,199,200,201,202,203,204,205,206,207,208,209,210,211,212,213,214,215,216,217,218,219,220,221,222,223,224,225,226,227,228,229,230,231,232,233,234,235,236,237,238,239,240,241,242,243,244,245,246,247,248,249,250,251,252,253,254,255,256,257,258,259,260,261,262,263,264,265,266,267,268,269,270,271,272,273,274,275,276,277,278,279,280,281,282,283,284,285,286,287,288,289,290,291,292,293,294,295,296,297,298,299,300,301,302,303,304,305,306,307,308,310,311,312,313,314,315,316,317,318,319,320,321,322,323,324,325,326,327,328,329,330,331,332,333,334,335,336,337,338,339,340,341,342,343,344,345,346,347,348,349,350,351,352,353,354,355,356,357,3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\ No newline at end of file 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6,278,299,300,312,326,336,349,355,361,362,363,365,366,367,370,395,416,417,424,466,467,469,471,472,474,477,479],affin:[16,17,18,220,370,386],afil:233,aforement:18,afresh:[287,477,495],afshar:391,after:[2,3,5,6,8,9,11,12,15,21,22,33,39,40,41,44,50,57,58,59,61,63,71,146,147,148,149,150,151,152,155,156,157,158,160,161,168,169,171,172,175,176,181,190,191,192,193,194,195,197,198,199,203,204,206,207,214,215,216,217,218,220,224,231,242,243,244,245,246,251,252,253,255,261,262,263,269,274,275,276,278,281,285,289,297,299,302,310,315,317,318,319,321,322,323,324,325,329,331,333,337,340,341,347,354,360,361,363,364,366,368,369,370,371,372,377,384,386,393,394,395,396,402,403,404,415,416,417,419,420,421,422,426,430,432,433,440,441,451,453,454,455,458,464,466,468,469,470,471,472,474,475,477,479,481,483,486,487,490,494,495,496,497,498,499],afterrun:477,afterward:3,afterword:41,ag1:167,ag2:167,again:[6,11,12,16,17,62,142,148,154,162,191,194,220,235,285,340,354,365,416,417,464,466,467,469,471,476,483,485,495,497],against:[11,12,13,64,221,365,432,433],aggreg:[6,12,65,68,69,79,93,110,117,235,251,297,299,312,464,496],aggress:[235,483],agilio:[9,13],agre:[3,8,188,363,372,404,433],agreement:[5,7],ahd:401,ahead:333,aidan:[0,5,7,9,13,358],aij:13,aim:6,airebo:[],ajaramil:[7,9,13],aka:193,akohlmei:[7,9,13,195,236],aktulga:[7,9,292,433],al2o3:440,al2o3_001:[120,300],al3:167,ala:[242,440],alain:9,alat:[280,419],alb:[430,453,455],albeit:298,albert:9,alchem:[87,162],alcohol:329,alcu:[371,377],alcu_eam:430,alderton:390,alejandr:[255,256],alessandro:13,algebra:422,algorithm:[0,1,6,7,8,9,41,61,194,203,214,217,220,242,244,245,269,282,290,299,302,321,322,326,329,334,361,362,363,367,370,395,417,422,437,439,464,466,483],alia:[12,16],alias:[1,356],aliceblu:194,align:[6,12,29,41,71,170,188,210,214,237,358,469,472,490],alkali:395,all:[0,1,2,3,5,6,7,8,9,11,12,13,14,15,16,17,18,22,33,37,39,40,41,42,44,50,54,55,57,59,60,61,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,156,161,162,163,164,165,166,167,168,169,170,171,172,174,176,181,187,188,191,192,193,194,195,197,198,199,200,202,203,204,205,206,207,208,209,210,211,212,213,214,215,216,217,218,219,220,221,223,224,225,226,227,228,229,231,232,233,234,235,236,237,238,239,240,241,242,243,244,245,248,250,251,253,255,256,257,258,259,260,261,262,263,264,265,266,267,268,269,270,272,273,274,275,276,277,278,279,280,281,282,284,285,286,287,288,289,290,291,292,294,295,296,297,298,299,300,301,302,303,304,305,306,310,311,313,314,315,316,317,318,321,322,323,324,325,326,327,328,329,331,332,333,334,335,336,337,338,339,340,341,345,350,353,354,355,356,357,358,360,363,364,365,366,367,369,370,371,372,373,375,376,377,378,380,381,382,383,384,386,387,390,391,392,393,394,395,396,397,398,399,400,401,402,403,404,405,406,407,408,409,411,415,416,417,418,419,420,421,422,423,424,425,426,427,429,430,431,432,433,434,435,440,441,442,443,444,445,446,447,448,449,450,451,452,453,454,455,456,457,458,459,461,462,463,464,466,467,468,469,470,471,472,473,474,476,477,478,479,480,481,482,483,484,486,487,488,490,494,495,496,497,498,499],allen:[29,87,390,398],allentildeslei:87,allign:3,allindex:338,alloc:[3,5,6,8,9,11,12,60,229,328,364,366,370,428,433,469,477],allocat:3,alloi:[],allosw:71,allow:[1,2,3,6,8,9,11,12,13,14,15,16,17,18,22,37,39,40,41,55,57,58,59,61,62,63,77,92,108,110,144,146,147,148,161,166,167,168,170,176,187,188,191,193,194,195,197,198,200,202,203,204,206,207,208,209,210,211,212,214,216,217,218,219,220,221,225,226,229,231,232,233,234,236,239,242,245,246,250,252,255,256,280,284,285,286,287,288,289,293,299,300,302,303,305,306,310,314,321,322,323,324,326,327,328,329,330,331,337,339,341,350,355,356,358,363,364,365,366,369,370,373,377,378,379,380,381,382,387,393,395,399,400,401,402,407,411,416,417,422,424,430,433,434,437,439,440,449,459,461,464,467,469,471,472,473,474,475,476,479,481,482,483,486,487,495,496],almost:[2,3,12,60,237,289,326,356,367,370,449],alo:387,alon:[6,7,217,295,432,433,467],alond:13,along:[6,8,9,12,29,40,71,87,120,166,167,168,190,191,193,206,217,237,242,243,247,252,254,289,299,302,303,307,311,312,321,325,326,332,335,337,358,361,362,363,365,387,390,399,402,405,407,411,419,432,433,452,469,472,479,480,495],alonso:[420,421],alpha:[6,12,51,198,242,281,289,290,294,363,371,374,378,387,391,393,394,396,401,406,407,419,425,429,454,456,487,490],alpha_:[],alpha_c:415,alpha_i:441,alpha_ialpha_j:[],alpha_lj:415,alphabet:[2,3,22,37,44,55,63,176,187,197,341,350,364,384,450,469],alphanumer:[3,63,197,288,296,339,364,495],alreadi:[3,7,8,9,12,16,17,18,42,168,169,171,192,202,206,210,211,214,216,220,246,287,289,314,337,364,365,391,400,402,409,417,449,459,462,465,469,470,474,479,495],also:[0,1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,22,29,36,37,38,39,40,41,42,44,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008:[432,433],chi:[93,157,190,280,290,292,396,398,496],chiefli:431,child:8,chip:[7,12,17,18,370,482],chipot:219,chiral:349,chmod:[11,12],cho:419,chocol:[7,194],choic:[3,6,12,15,16,18,40,41,54,87,143,146,147,161,172,188,206,210,211,214,217,220,221,233,239,242,253,255,282,290,299,321,350,356,361,362,365,367,370,402,415,424,428,469,478,479,482,483,489,490,494],choos:[1,3,6,7,8,12,16,17,18,29,39,54,87,119,158,159,193,215,216,217,218,221,228,239,242,253,255,257,258,259,260,261,262,263,285,286,314,318,332,355,356,362,459,464,466,478,484],chose:[453,455],chosen:[2,3,6,12,17,142,168,171,180,188,193,199,204,218,221,228,231,232,240,242,253,255,260,282,285,296,314,318,321,322,327,329,330,336,356,357,362,370,395,399,406,409,435,453,464,478,483,490],chri:166,christian:[7,9,14,17],christoph:7,chunk:[],chunkid:[66,75,90,94,105,107,116,148,163,165,206],chute:[4,10,234],ciccotti:302,cieplak:[6,174,481],cii:207,cij:207,circl:[42,71,310],circular:[3,6,146,189],circumst:18,circumv:[92,108,294],citat:[],cite:[3,7,8,12,239,440],ckio:2,cko:2,cl1:167,clarendon:[29,390],clarifi:[7,453,455],clariti:339,clark:427,class2:[],classic:[0,3,5,6,7,8,9,229,282,289,294,326,351,395],classifi:[9,450,458],claus:467,clean:[6,12,14,15,17,477],cleanli:[468,498],clear:[],clearli:7,clebsch:142,clermont:[9,13],clever:473,click:[2,11,22,37,44,55,168,176,187,193,236,341,350,365,384,450],client:[236,238],climb:[254,365,483],clinic:[7,13],clo:[157,190,496],clock:[12,464,483],clockwis:332,close:[3,6,11,12,13,39,41,67,71,143,171,191,216,217,218,233,240,242,255,276,299,302,332,335,354,356,359,361,362,365,370,372,377,387,388,405,419,424,436,438,455,473,479,490,492],closer:[3,41,118,166,190,191,214,218,222,323,365],closest:[216,280,299,329,398,434,449,459],cloud:[440,490],clovertown:18,clsuter:72,clump1:[284,299],clump2:[284,299],clump3:[284,299],clump:299,cluster:[],clutter:[3,9],cmap:469,cmatrix:233,cmax:419,cmd:[11,12,282,480],cmdarg:11,cmin:419,cmm:[],cmoput:135,cn1:207,cn2:207,cna:[],cnn:207,cnr:[9,13],cnt:[402,473],co2:[40,167,302,364],coars:[7,9,29,36,40,54,180,284,299,314,400,435,481],coarser:[356,495],coarsest:142,code:[],coeff:[3,7,8,12,21,22,33,44,50,174,175,176,181,340,341,347,384,402,406,424,437,439,442,469],coeffcient:469,coeffici:[],coefficienct:391,coefficient0:393,coefficient1:393,coeffieci:[6,374,405],coeffincientn:393,coexist:[9,231,395],cohes:[6,396,419],coincid:[124,335,382,416,417,464],colberg:192,cold:[6,153,231,235,366,490],coldest:322,coleman8:9,coleman:[9,120,167,300],colin:9,collabor:[7,8,9,15],collect:[3,6,7,8,9,13,40,42,66,75,83,90,94,99,105,107,116,148,156,163,165,168,191,194,206,219,245,251,284,294,297,299,337,355,364,366,385,469,476,482,488,499],collid:[225,314,336],colliex:167,collinear:[3,284],collis:[3,242,314,332,336,392,399,462],colllis:314,colloid:[],colombo:39,colon:[195,337,470],color1:194,color2:194,color:[3,9,41,191,193,194,214,232,289,294],column:[3,6,9,12,13,42,63,65,66,67,68,69,71,75,77,79,81,90,92,93,94,105,107,108,110,112,115,116,117,118,119,121,142,143,148,156,163,165,166,167,188,191,194,197,205,206,207,209,210,211,212,245,252,253,289,299,315,316,326,336,397,401,432,433,470,484,486,495],columnar:166,colvar:[],colvarmodul:12,com:[],comamnd:220,comand:217,comannd:370,comb3:[],comb:[],comb_1:291,comb_2:291,combiant:388,combin:[3,6,7,9,11,13,36,40,63,65,69,79,87,93,104,110,117,146,147,161,191,193,203,209,236,245,255,282,288,318,327,335,338,340,355,356,358,362,370,385,387,388,395,396,402,414,415,441,451,453,455,458,461,472,477,482,490,495],come:[],comfort:[12,13],comm:[0,3,11,12,61,73,192,236,238,239,356,365,370,391,424,429,452,471],comm_modifi:[],comm_modift:61,comm_styl:[],comm_world:11,command:[],comment:[2,7,11,12,38,56,174,188,191,240,299,326,364,365,371,393,394,396,406,419,426,433,440,441,451,452,453,454,455,458,466,467,469,490,495],commerci:7,commmand:[3,6,12,59,109,277,405,463,464,466,483,498],common:[],commonli:[3,6,12,17,25,57,59,106,108,170,191,193,195,351,400,409,441,453,455,469,472,481],commun:[1,3,6,7,8,10,11,12,14,15,16,18,40,41,58,61,62,71,166,171,172,193,194,214,215,216,218,219,220,236,238,242,244,245,246,255,281,288,290,291,292,299,314,326,337,353,355,366,367,368,370,392,428,466,467,478,479,495,497,499],communc:355,comp:[7,192,238,239,302,356,365,395,424,429,434,448,452,454],compact:[63,197,384,450],compani:[5,7],compar:[1,3,4,6,8,12,17,39,86,112,120,151,167,176,187,194,224,290,337,339,355,356,363,365,419,440,464,483,484,490,494],comparison:[],comparison_of_nvidia_graphics_processing_unit:14,compass:[7,21,22,37,43,44,55,175,176,187,340,341,350,383,450],compat:[3,5,7,8,9,11,12,13,17,18,41,71,119,121,179,191,195,199,205,206,207,209,210,211,212,214,281,293,318,321,328,331,334,355,370,403,422,424,452,466,467,495],compens:[6,215,216,297,366,395],compet:325,competit:356,compil:[3,7,8,9,10,12,13,14,15,16,17,18,19,166,191,192,193,195,236,325,356,370,422,469,470,474,495],compl:17,complain:[12,17],complement:419,complementari:[7,387,407],complet:[3,6,9,11,12,15,41,59,71,194,210,214,219,245,282,285,288,314,325,327,339,354,365,370,396,437,439,457,464,469,474,477,481,483,486,490,495],complex:[6,8,11,12,13,25,40,42,62,92,108,142,144,156,168,169,242,310,335,353,365,395,422,452,467,469,472,495],compli:[321,325],complic:[6,7,9,12,13,204,231,467],complier:12,compon:[3,6,8,12,61,63,66,67,73,81,88,89,90,91,92,94,95,98,105,106,107,108,109,110,111,112,114,115,119,129,132,133,134,135,138,139,140,142,143,145,146,147,148,149,150,151,152,153,154,155,156,157,158,160,161,163,164,165,190,191,193,194,200,201,205,206,207,208,209,210,211,212,213,217,218,220,221,226,229,234,238,239,242,245,247,251,252,254,255,256,260,261,262,263,274,275,276,278,279,281,282,283,286,297,299,301,302,303,307,308,311,314,317,318,319,321,328,329,334,335,336,355,358,362,363,364,365,370,376,391,395,399,416,417,437,439,440,441,469,470,479,487,495,496],componenet:6,composit:[6,204,242,393],compound:[386,395,396,458],compres:[71,116,206],compress:[],compris:[40,335,434,457],compton:[120,167],comptu:3,compuat:356,comput:[],computation:[3,6,215,216,326,377],computational:490,compute_arrai:8,compute_fep:[199,415],compute_group_group:231,compute_inn:8,compute_ke_atom:8,compute_loc:8,compute_modifi:[],compute_peratom:8,compute_sa:[120,300],compute_scalar:8,compute_temp:8,compute_ti:199,compute_vector:8,compute_xrd:167,concaten:[2,3,498],concav:335,concentr:[71,393],concept:[6,148,158,206,478],conceptu:[3,6,71,156,218,220,365,387,402,419,474],concern:[6,73,87,192,232],concetr:71,concis:[11,325],conclud:12,concret:8,concurr:[9,16,356,495],conden:[326,453,455],condens:[6,150,326,372,389,393,407,458],condit:[],conducit:6,conduct:[],cone:472,confer:422,confid:[3,483],config:[12,191,466],configfil:219,configur:[1,2,6,12,15,17,38,59,124,170,188,190,191,193,197,218,219,220,221,225,231,238,239,269,282,290,325,353,363,365,372,377,394,419,422,451,453,455,458,464,469,471,472,483],confin:[469,483],conflict:[3,12,40,424,467],conform:[3,6,13,59,217,218,254,298,303,325,349,365,395,481],confus:[3,458],conjuct:391,conjug:[7,8,239,362,395,432,433],conjunct:[6,7,71,86,87,116,151,156,162,168,172,194,198,199,239,242,246,269,285,286,290,291,292,294,299,314,322,329,334,355,356,365,378,380,384,387,391,395,401,407,424,427,435,456,469,472,476,490,499],connect:[3,6,87,153,171,217,236,284,299,302,311,365,388,399,449,455,466,467,473,490],conput:3,consecut:[3,11,12,39,71,168,194,198,199,221,236,237,387,407,411,464,470,472],consequ:[1,6,204,326,406,483],conserv:[3,29,197,204,217,224,225,232,235,239,241,242,246,251,253,255,269,299,302,317,318,322,329,330,334,365,390,391,399,413,440,478,483],consid:[6,9,70,71,78,87,117,150,153,154,171,191,194,198,199,205,207,210,214,216,217,221,243,256,281,299,321,322,325,326,329,356,384,395,402,433,434,440,449,464,465,467,470,471,472,474,477,479,487,490,495],consider:[6,8,239,240,317,318,319,370,478],consist:[3,6,8,9,11,12,40,42,65,69,79,93,105,110,113,114,117,148,151,153,168,180,190,195,200,201,206,220,221,224,226,229,232,239,240,241,252,255,257,258,259,260,261,262,263,264,265,267,268,269,270,272,273,274,275,276,277,278,286,289,294,296,298,299,317,318,319,320,330,355,356,358,364,365,370,372,377,379,385,387,395,398,402,405,416,417,419,422,424,434,437,439,440,452,459,467,469,470,471,472,473,474,481,490,495],consistent_fe_initi:203,consit:299,constant:[],constitu:[3,6,245,299,331,335,385,434],constitut:[437,439],constrain:[3,6,8,145,146,147,148,149,151,154,155,156,157,158,160,161,197,206,221,231,232,237,245,249,284,285,297,299,302,312,322,329,363,364,395,474,481,490],constraint:[],construct:[6,8,12,14,38,54,56,61,64,67,70,72,73,77,92,108,120,142,167,218,255,281,298,335,366,370,390,422,424,449,451,452,472,473,488,495],constructor:[8,11],consult:433,consum:[1,294,428,495],consumpt:353,contact:[],contact_stiff:[436,438],contain:[0,1,2,3,4,6,8,9,11,12,13,17,18,19,38,40,41,56,63,87,91,118,120,142,148,156,166,167,168,170,174,176,187,188,191,193,194,195,197,198,199,203,205,206,207,209,210,211,212,214,219,221,226,233,237,238,239,242,253,269,280,281,284,285,287,289,292,296,299,300,304,314,321,325,326,335,336,339,354,356,364,365,368,369,371,372,373,377,386,387,390,393,394,395,402,403,419,422,426,430,431,432,433,441,451,452,453,454,455,456,458,464,465,466,467,469,470,471,472,474,476,478,481,483,486,487,490,495,497,499],content:[12,18,433,485,487],context:[3,6,8,12,17,118,119,194,215,216,221,284,296,330,362,461,469,476,485,494,495,496],contibut:70,contigu:466,contin:16,continu:[0,2,3,5,6,9,12,13,14,41,71,81,104,105,164,194,197,198,199,204,206,207,208,209,210,211,212,214,217,218,219,220,221,231,232,233,235,236,237,239,240,241,247,252,253,255,257,258,259,260,261,262,263,274,275,276,277,278,283,285,288,289,299,300,303,313,314,316,323,324,326,332,335,339,354,369,370,377,391,392,409,412,432,433,434,437,439,454,464,467,469,471,472,477,483,486,487,495,497],continuum:[6,7,9,203,326,437,439],contour_integr:203,contract:[59,218,220,255,286,299],contradictori:3,contrain:302,contraint:269,contrari:[233,240],contrast:[1,6,42,55,64,150,153,220,337,437,439,461,498],contrib:326,contribut:[3,5,6,7,8,9,12,13,17,63,66,68,70,71,74,75,77,80,84,87,88,89,90,91,94,103,105,107,109,110,111,112,114,116,119,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,199,204,205,206,207,209,210,211,212,218,231,239,242,245,246,250,256,276,277,284,285,293,296,299,300,302,328,355,363,365,373,391,392,393,395,402,416,417,422,424,432,433,440,481,487,490],contributor:12,control:[3,5,6,7,8,9,11,13,16,27,29,41,87,91,124,142,177,191,193,197,203,204,214,218,219,220,235,236,239,240,255,257,258,259,260,261,262,263,286,291,299,305,306,317,318,319,326,330,353,355,367,395,398,422,432,433,436,438,451,455,464,466,478,484,485],control_typ:203,controlfil:433,convect:91,conveni:[6,12,29,191,195,212,300,358,441,495],convent:[3,8,9,29,179,186,187,194,298,311,338,393,395,495],converg:[3,6,41,88,191,193,195,200,214,217,218,226,229,260,289,291,294,298,302,361,362,363,365,386,387,407,440,464,476,483],convers:[3,8,142,193,194,204,207,286,355,387,388,389,395,407,411,415,427,467,483,494],convert:[2,3,4,5,6,7,8,12,13,20,21,24,28,32,35,36,59,63,71,91,168,175,191,193,194,212,253,285,337,340,342,346,349,358,365,371,393,422,453,455,462,467,469,470,471,476,486,490,494,495,497,499],convex:[42,335,376],convinc:[7,12],cook:9,cooki:7,cool:[7,158,235,297],cooordin:191,cooper:[5,7],coord123:116,coord1:[3,116,206,210,211],coord2:[3,116,206,210,211],coord3:[3,116,206,210,211],coord:[],coordb:440,coordbb:440,coordiat:363,coordin:[1,3,4,6,7,8,11,13,14,15,17,40,41,42,59,61,62,63,66,68,71,74,75,77,81,87,89,90,94,104,105,107,115,116,118,136,142,151,157,163,165,166,168,172,190,191,192,193,194,195,197,200,205,206,209,210,211,214,215,216,217,218,219,220,221,224,226,227,229,231,234,235,236,237,238,239,240,252,254,255,257,258,259,261,262,263,276,279,280,281,284,285,286,296,297,299,301,302,303,308,311,312,313,314,316,324,325,326,333,334,336,337,358,363,364,365,370,371,372,375,376,394,440,464,469,470,471,472,474,477,479,483,490,495,496],coordn:[116,206],coorind:[],copi:[0,3,4,8,11,12,15,17,40,121,193,326,365,384,432,467],copper:462,coproccesor:16,coprocessor:[1,4,7,9,16,17,370,482],coproprocessor:17,copy_arrai:8,copyright:[7,8,284],coral:194,core:[],core_shel:150,coreshel:[6,9,380,387,389],cornel:[6,174,481],corner123i:115,corner123x:115,corner123z:115,corner1i:115,corner1x:115,corner1z:115,corner2i:115,corner2x:115,corner2z:115,corner3i:115,corner3x:115,corner3z:115,corner:[3,6,40,115,193,335,336,358,457,469],cornflowerblu:194,cornsilk:194,corpor:16,corr:386,correct:[3,6,9,11,12,16,17,59,87,88,103,104,112,118,150,155,162,193,220,231,233,239,255,256,276,284,286,289,325,331,335,355,365,371,372,373,374,375,376,377,378,379,380,381,382,383,385,386,387,388,389,390,391,392,393,394,395,397,398,399,400,401,402,403,404,405,406,407,408,409,410,411,412,413,414,415,416,417,418,419,420,421,422,423,424,425,427,429,430,431,432,433,434,435,436,437,438,439,440,441,442,443,444,445,446,447,448,449,450,451,452,453,454,455,457,458,460,461,462,469,484,487,490],correction_max_iter:203,correctli:[3,8,9,11,17,71,81,103,104,105,145,146,147,149,151,153,154,155,156,157,160,161,164,191,194,200,221,226,229,240,249,255,256,292,299,302,311,313,332,335,365,366,370,389,417,422,466,467,469,479,494,496],correl:[],correspond:[1,2,6,8,11,12,14,20,21,22,23,24,25,26,27,28,29,30,31,32,35,38,40,42,43,44,45,46,47,48,49,51,53,54,56,70,71,87,97,98,111,114,115,116,117,120,121,129,132,133,134,135,136,138,139,140,142,145,146,155,162,166,167,174,175,176,177,178,179,180,182,183,185,186,188,190,191,193,194,198,199,200,206,208,209,210,211,213,216,218,220,227,229,230,234,239,242,243,251,252,253,255,257,258,259,260,261,262,263,264,265,269,272,274,275,276,278,281,282,286,291,299,301,302,317,319,321,330,331,332,334,335,336,338,340,341,342,343,345,346,349,351,356,360,362,364,365,371,372,374,378,379,380,381,382,383,384,385,386,387,390,391,393,394,395,396,397,398,399,400,401,402,405,407,408,409,410,411,412,413,414,415,416,419,420,422,424,425,426,427,429,430,432,433,434,435,440,441,442,451,452,453,454,455,458,460,461,462,464,466,467,469,470,472,482,483,484,486,487,490,495],correspondingli:[416,417,478],cosin:[],cosineshift:27,cosmo:[233,238],cossq:[],cost:[1,6,10,11,12,17,39,41,71,111,120,143,167,193,194,206,210,211,214,215,216,228,255,291,326,355,356,368,387,407,411,422,424,451,466,478],costheta0:[451,453,455,458],costheta:430,costli:[11,88,233,366],couett:4,coul:[],could:[2,3,6,9,11,12,17,33,41,50,59,66,71,75,87,90,94,105,107,111,114,116,148,158,163,165,181,191,193,194,198,199,206,207,210,214,220,229,238,288,289,290,294,297,299,301,314,315,321,325,326,327,331,335,337,339,347,352,354,361,363,366,370,373,397,401,402,405,432,433,465,466,467,469,471,473,476,477,485,490,495,496],coulomb:[3,5,6,7,8,9,10,12,14,15,18,72,88,109,110,118,143,169,173,290,292,327,355,356,363,370,378,380,381,382,383,386,387,388,389,390,395,399,400,402,407,411,415,418,424,427,432,433,435,440,450,455,456,458,461,474,481,487,490,494],coulommb:6,cound:3,count:[1,3,6,8,10,11,12,16,41,63,68,77,91,116,118,119,156,166,172,200,201,204,206,209,210,211,213,214,221,226,228,231,237,255,269,285,302,317,318,335,356,363,364,365,367,370,397,401,424,487,495],counter:[332,464,475,477,483],counteract:231,counterbal:235,counterbalanc:29,counterpart:[191,299,464],counterproduct:18,coupl:[],courant:304,cours:[3,8,128,130,162,191,198,199,232,298,311,325,331,333,334,336,337,356,416,442,466,469,482,490,495,497],courtesi:358,cov:440,coval:[6,29,395,419,440,490],covari:233,cover:[6,71,188,194,203,242,395,457],coverag:[71,210],cpc:238,cpp:[1,3,6,8,9,11,12,13,87,191,198,199,229,302],cpu:[1,3,4,9,10,12,14,15,16,17,18,63,71,194,208,224,240,327,353,356,370,384,450,464,482,483,486,487,488,495],cpuremain:487,cr2:167,cr3:167,crack:[4,366],crada:[5,7],crai:[5,7,13,18,191],crash:[3,12,366,490],craympi:370,creat:[],create_atom:[],create_bond:[],create_box:[],create_elementset:203,create_faceset:203,create_group:192,create_nodeset:203,createatom:[],creation:[],crimson:194,critchlei:284,criteria:[3,118,169,193,194,215,216,217,250,363,429,457,471,474,495],criterion:[12,41,123,168,171,204,214,217,231,269,291,304,332,337,363,365,386,395,399,440,474,483,484],criterioni:483,critic:[6,48,49,253,321,326,363],crmax:71,crmin:71,cross:[3,12,22,71,89,146,166,176,191,193,205,210,216,220,252,254,276,299,307,311,313,322,329,341,358,365,382,391,392,393,400,401,402,407,409,411,430,435,437,439,453,455,462,469,473,479,497],crossov:1,crossterm:469,crozier:[0,7,13],crucial:289,crystal:[4,6,13,73,108,280,281,324,358,366,473,487,490],crystallin:[6,104,281,358,454,490],crystallis:321,crystallogr:[120,167],crystallograph:[358,487],crystallographi:[120,167,358],cs1:167,cs_chunk:6,cs_im:[40,469],cs_re:[40,469],csanyi:[142,431,441],cscl:419,csequ:6,csh:[11,12,384],cshrc:[11,12],csic:[394,451,453,455,458],csinfo:6,csisi:[394,451,453,455,458],csld:[],cst:393,cstherm:6,cstyle:466,csvr:[],ctcm:[371,393],ctemp_cor:224,cterm:303,ctr:9,ctype:11,cu1:167,cu2:167,cu3au:419,cube:[6,41,166,171,214,224,335,358,490],cubic:[],cuda:[],cuda_arch:15,cuda_get:15,cuda_hom:15,cuda_prec:15,cufft:14,cuh:377,cummul:[3,6,212,215,216,217,219,228,233,239,241,314,317,318,319,320,322,329,401,487],cumul:[6,204,206,209,210,211,225,231,239,253,255,260,269,299,300,365],curli:2,current:[0,1,3,5,6,7,8,9,11,12,13,15,16,17,18,40,41,42,59,61,63,71,73,81,87,103,104,110,118,119,132,143,148,156,158,164,166,169,172,190,191,192,193,194,195,198,199,203,206,210,211,212,214,215,216,217,218,219,220,221,225,226,229,231,233,236,237,239,245,252,255,256,261,262,263,269,274,275,276,278,284,285,290,291,293,296,297,298,299,302,303,304,305,306,307,308,310,312,313,314,317,318,319,325,326,329,330,331,332,333,334,336,337,339,353,354,355,356,359,360,362,363,364,365,370,376,377,384,386,390,393,395,396,399,402,403,406,416,417,419,420,421,424,430,432,433,436,437,438,439,442,453,455,456,459,464,465,466,467,469,470,471,472,473,475,476,477,479,481,483,484,486,487,495,496,497,498,499],curv:[6,168,231,281],curvatur:[398,434,462],custom:[],cut0:467,cut1:478,cut2:478,cut:[],cuthi:[280,292],cutinn:[379,416,417],cutlo:[280,292],cutmax:430,cutoff1:[383,390,407,411,415,418,427,435],cutoff2:[378,380,381,383,389,390,407,411,415,418,427,435],cutoff:[3,6,10,16,18,39,45,46,54,55,61,70,72,73,77,87,92,108,110,117,118,142,166,169,171,172,216,217,222,280,289,290,292,294,296,299,314,327,331,335,337,353,355,356,363,366,367,368,370,371,372,373,374,375,376,377,378,379,380,381,382,383,385,387,388,389,390,391,392,393,394,395,396,397,398,400,401,402,403,405,406,407,408,409,410,411,412,413,414,415,416,417,418,419,420,421,422,423,424,425,426,427,428,429,430,432,433,434,435,440,441,442,443,444,445,447,448,449,450,451,452,453,454,455,456,457,458,459,460,461,462,467,471,474,478,490,495],cutoff_glob:376,cutoff_inn:376,cutoffa:394,cutoffc:394,cuu3:393,cval:167,cvd:321,cvel:303,cvff:[],cwiggl:[3,252,331,334,336,495],cyan:[2,193,194],cycl:[3,231,253,255,256,260],cyclic:[3,188],cygwin:12,cylind:[3,4,71,193,206,237,285,332,335,472],cylindr:[6,237,311,332],cypress:370,cyrot:377,cyrstal:281,d3q15:242,d3q19:242,d_double_doubl:15,d_e:326,d_flag2:288,d_flag:288,d_name:[115,191,288,316,479],d_single_doubl:15,d_single_singl:15,d_sx:288,d_sy:288,d_sz:288,daan:324,dai:12,daili:12,daivi:276,damag:[],dammak:294,damp:[3,6,197,202,239,240,241,246,255,256,260,286,289,290,294,299,317,318,330,332,333,362,363,365,378,380,382,387,390,395,399,407,415,427,435,450,456,483,490],damp_com:240,damp_drud:240,dampen:[299,490],dampflag:[332,399],dan:17,danger:[3,12,231,337,391,487],dangl:171,daniel:9,darden:[356,390],darkblu:194,darkcyan:194,darken:193,darkgoldenrod:194,darkgrai:194,darkgreen:194,darkkhaki:194,darkmagenta:194,darkolivegreen:194,darkorang:194,darkorchid:194,darkr:194,darksalmon:194,darkseagreen:194,darkslateblu:194,darkslategrai:194,darkturquois:194,darkviolet:194,dasgupta:290,dash:[399,486],dat:[6,91,188,203,465],data2xmovi:[],data:[],data_atom:8,data_atom_hybrid:8,data_bodi:8,data_vel:8,data_vel_hybrid:8,databas:[],datafil:[12,13,300],dataset:300,datatyp:3,date:[0,6,12,13,190,432,433,495],datom1:117,datom2:117,datom3:117,datom4:117,datum:[3,6,42,65,68,69,79,93,110,117,191,207],davenport:418,davi:331,david:[9,19,355,356,453,455],daw:[393,430],dbg:14,dcd:[3,6,7,191,192,193,194,195,282,470,474],ddim:190,deactiv:415,dealt:238,debug:[6,7,11,12,13,14,17,120,124,167,168,282,287,353,355,370,403,424,459,467,468,476,479,486,495],deby:[],decai:[92,387,462],decid:[3,6,12,16,71,252,288,299,327,484],decipher:358,declar:192,declin:314,decod:193,decompos:[87,441],decomposit:[3,5,7,18,62,203,282],decoupl:[6,490],decreas:[3,191,200,201,208,217,220,226,229,231,239,325,355],decrement:303,deepli:352,deeppink:194,deepskyblu:194,def:[12,13,467],defaul:61,defect:[6,70,166,422],defgrad:2,defin:[2,3,5,6,7,8,11,12,17,20,21,22,23,24,25,26,27,28,29,30,31,32,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,51,53,54,55,56,57,58,59,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167,168,169,170,171,172,174,175,176,177,178,179,180,182,183,185,186,187,188,189,190,191,192,193,194,197,198,199,200,201,202,203,204,205,206,207,209,210,211,212,213,214,215,216,217,218,220,221,224,225,226,229,230,231,234,237,238,239,240,241,242,250,252,254,255,256,257,258,259,260,261,262,263,265,266,267,270,272,273,274,275,276,277,278,280,281,282,284,285,286,288,290,292,297,299,300,301,302,304,308,312,314,316,317,318,319,320,322,323,324,326,328,329,331,332,333,334,335,336,337,339,340,341,342,343,344,345,346,349,350,351,353,355,356,358,360,362,363,364,365,366,367,368,369,370,372,373,374,375,376,378,379,380,381,382,383,384,385,387,388,390,391,392,394,395,397,398,399,400,401,402,403,405,407,408,409,410,411,412,413,414,415,416,417,418,422,423,424,425,426,427,429,430,432,433,434,435,436,437,438,439,441,442,443,444,445,446,447,448,449,450,451,452,453,454,455,456,457,458,459,460,461,462,463,464,466,467,469,470,472,473,474,475,478,479,480,481,483,484,486,487,490,491,492,493,494,495,496],definit:[2,3,6,8,12,13,78,80,118,142,194,206,207,208,209,210,211,212,220,237,260,300,316,328,331,334,336,338,350,353,364,373,377,385,395,405,430,437,439,441,457,467,469,471,478,480,494,495],defint:487,deform:[],deg2theta:167,deg:490,degener:[3,284],degrad:[8,18,281,356,478],degre:[3,6,8,20,21,24,28,29,32,35,36,38,65,79,92,93,95,97,98,100,102,103,108,114,145,146,147,148,149,150,151,152,153,154,155,156,157,158,160,161,167,168,174,175,178,179,186,188,190,193,206,217,224,231,233,234,239,240,245,255,256,260,261,262,263,274,275,276,278,282,284,298,299,302,317,318,319,324,340,342,346,349,351,363,390,393,401,479,487,490,496],degress:[148,206],del:483,delai:[3,6,12,366,392,487],deleg:402,delet:[2,3,7,8,12,54,57,60,63,166,171,172,197,206,207,209,210,211,212,215,217,228,231,255,300,317,318,337,339,354,364,366,369,424,449,469,470,471,472,480,481,486,491,493,495,496],delete_atom:[],delete_bond:[],delete_el:203,deli:190,delimit:[467,495],deloc:[256,395,440],delr:419,delt_lo:483,delta:[],delta_1:377,delta_3:377,delta_7:377,delta_conf:3,delta_ij:[419,430],delta_mu:3,delta_pi:377,delta_r:430,delta_sigma:377,delta_ua:376,delx:190,delz:190,dem:376,demand:294,demo:11,demon:279,demonstr:[289,419],den:285,dendrim:401,denniston:[9,242,244,245,246,281],denomin:[7,173],denot:[120,224,240,281,292,294,387,400,402,433,437,439],dens:[71,217,395],densiti:[3,6,7,9,18,40,41,59,101,118,128,142,154,166,168,198,199,203,206,210,211,214,220,229,242,245,248,249,281,285,286,290,326,331,358,360,364,371,377,393,419,420,421,430,434,440,444,446,447,448,469,478,479,487,494],density_continu:439,density_summ:439,depart:[0,7],departur:[253,289],depend:[1,2,3,6,8,9,11,12,16,17,18,20,21,22,23,24,25,26,27,28,29,30,31,32,35,38,39,40,41,43,44,45,46,47,48,49,51,53,54,56,61,63,65,68,69,70,71,79,92,93,104,110,111,114,115,116,117,121,142,145,151,155,156,162,168,169,174,175,176,177,178,179,180,182,183,185,186,187,188,190,191,193,194,197,198,199,200,201,204,206,208,209,210,212,213,214,216,218,220,226,227,230,233,234,235,237,239,240,242,244,245,252,255,257,258,259,260,261,262,263,264,265,272,274,275,276,278,280,291,294,296,299,301,302,308,314,317,318,319,321,323,325,326,328,330,331,334,335,336,337,339,340,341,342,343,345,346,349,351,356,358,363,364,366,367,368,370,371,372,374,375,377,378,379,380,381,382,383,384,385,386,387,388,390,391,393,394,395,396,397,398,399,400,401,402,407,408,409,410,411,412,413,414,415,416,419,420,422,423,425,426,427,429,430,432,433,434,435,440,441,442,450,451,452,453,454,455,456,458,460,461,462,464,466,469,471,472,475,479,481,483,486,487,489,495,496],dependend:6,depflag:12,dephas:[464,483],depos:221,deposit:[],deprec:[290,432],depth:[51,146,193,326,398,434],dequidt:9,der:[87,109,385,386,415,432,433,461,490],deriv:[6,7,8,9,38,56,63,87,142,162,188,207,218,220,231,239,252,255,257,258,259,260,261,262,263,280,286,290,294,323,324,326,331,332,335,362,364,372,377,385,390,395,396,400,409,413,414,419,422,432,433,450,452,461,490],derjagin:461,derlet:280,descend:194,descent:[7,362],descib:[40,193,290],describ:[0,1,2,3,4,6,7,8,9,10,11,12,13,14,15,16,17,18,19,38,39,40,41,42,56,62,63,68,70,71,73,88,112,115,118,120,132,142,143,146,147,148,152,153,156,159,161,162,166,167,168,170,171,180,185,188,191,192,197,198,199,206,207,208,209,210,211,212,214,217,218,219,220,221,223,224,232,233,236,237,238,239,240,241,242,244,245,246,250,254,255,256,260,268,277,280,282,287,288,289,290,291,292,299,303,311,314,315,316,317,318,319,320,321,322,323,324,329,331,332,334,339,355,356,358,361,362,363,364,365,369,372,373,375,376,378,379,380,382,383,384,385,386,387,390,393,395,396,398,399,400,402,405,407,408,409,410,411,412,413,414,415,416,417,418,419,422,423,429,430,431,432,433,434,435,440,441,442,449,450,451,452,453,454,455,456,458,460,461,462,464,466,467,469,470,471,472,473,479,482,483,486,495,496,497],descript:[],descriptor:[142,191,403],deserno:356,design:[0,3,6,7,8,9,11,13,14,15,17,120,150,153,167,203,217,223,224,255,256,280,281,300,321,326,373,374,375,376,379,382,387,389,395,415,416,417,420,421,430,433,452,478],desir:[2,3,6,7,11,12,14,15,16,33,40,50,59,71,88,91,114,119,143,150,168,181,190,206,212,218,220,229,231,232,239,240,241,245,255,276,284,285,286,287,290,294,299,302,314,317,318,319,320,325,332,347,352,355,356,358,361,363,364,365,391,393,401,416,417,451,453,455,465,466,467,469,473,478,483,484,486,487,495,496,497],desk:7,desktop:[4,6,7,10,12,193],despit:490,destabil:377,destre:349,destroi:[11,39,215,216],detail:[1,2,3,4,6,7,8,9,11,12,13,14,15,16,17,18,19,22,37,40,41,42,55,63,66,67,68,71,75,78,90,91,94,103,105,107,109,111,113,114,116,119,121,142,143,145,146,147,148,151,161,162,163,165,168,169,172,173,176,187,190,191,193,194,197,198,199,203,206,207,208,209,210,212,214,216,217,218,219,220,221,229,231,232,233,234,236,237,239,241,242,246,252,253,254,255,256,257,258,259,260,261,262,263,267,269,274,275,276,277,278,281,284,285,286,288,289,291,292,293,299,302,314,317,318,319,320,321,322,324,325,326,327,328,329,330,337,339,341,350,355,356,359,363,364,366,367,370,371,372,373,375,376,377,379,381,382,383,384,385,386,387,390,391,395,396,398,399,400,401,402,407,408,409,410,411,412,413,414,415,416,417,418,419,423,424,429,432,433,434,440,441,442,450,457,460,461,467,469,470,471,472,474,475,478,479,481,484,487,488,495,496,499],detect:[2,3,12,42,61,63,86,92,230,285,325,365,386,401,406,464,466,469,480,483,495],determ:370,determin:[1,3,6,8,9,12,15,39,40,42,51,57,58,59,61,62,68,71,87,103,109,111,114,120,121,129,143,156,157,166,167,168,190,191,193,194,195,196,200,201,202,205,206,207,208,209,210,211,212,213,214,218,220,221,224,226,231,234,235,237,239,240,245,250,252,253,255,261,262,263,274,275,276,278,280,282,285,286,289,296,297,298,299,300,301,304,306,308,314,317,318,319,321,327,328,331,332,333,334,335,336,337,350,355,356,358,364,366,367,370,372,373,381,386,390,392,393,397,399,402,403,411,419,422,424,433,434,440,449,452,456,461,466,469,470,472,474,476,479,483,485,486,488,494,495,496],detil:110,devan:[9,435],devanathan:455,develop:[0,3,5,6,7,8,9,11,12,14,15,16,17,18,19,42,236,260,284,289,290,293,372,377,395,421,422,440,458,471],devemi:9,deviat:[253,260,280,397],deviator:9,devic:[1,3,12,15,17,236,370],device_typ:370,devin:[291,386],devis:421,dfactor:193,dff:490,dfft_fftw2:12,dfft_fftw3:12,dfft_fftw:12,dfft_none:12,dfft_singl:[3,12,356],dfft_xxx:12,dfftw:12,dfftw_size:12,dft:[9,293,422],dhi:[59,190,220,285],dhug:[253,289],dhugoniot:[253,289],dia:419,diagnost:[],diagon:[3,6,83,142,143,144,218,255,286,299,329,437,439],diagonalstyl:441,diagram:[41,120,167,187,214,282],diallo:401,diam:[193,194,285,364],diamet:[3,6,40,42,115,168,191,193,194,198,199,239,285,299,314,316,330,332,364,376,385,398,399,409,434,457,461,469,470,479],diamond:[358,395,419],diamter:[40,285],dick:6,dicsuss:252,dictat:[204,253],did:[3,12,363,391,392,393,399,424,453,455,477],didn:3,die:18,diel:[],dielectr:[],diff:[3,6,12,164,328,355],differ:[1,2,3,4,6,7,8,9,10,11,12,14,15,16,17,18,22,37,38,39,41,42,54,55,56,61,64,68,70,71,87,92,95,97,98,122,142,145,146,147,148,149,151,154,155,156,157,158,160,161,162,168,169,171,176,187,188,190,191,193,194,197,199,202,204,206,209,214,215,216,217,218,219,220,224,230,231,232,233,234,235,236,239,240,242,252,255,256,257,258,259,261,262,263,265,267,270,272,273,274,275,278,280,282,284,286,289,290,291,294,297,299,302,303,311,312,314,317,318,319,322,323,324,326,329,330,331,332,335,339,340,350,352,354,355,356,358,359,361,362,364,365,367,368,369,370,371,372,377,381,382,384,385,386,391,393,395,398,399,400,402,405,407,408,410,411,418,419,420,421,423,424,426,430,432,433,434,435,436,437,439,440,441,442,450,451,452,453,455,457,458,461,463,464,466,467,469,471,472,473,474,477,478,479,481,483,484,486,487,488,490,494,495,496,497],differenti:[1,3,6,29,188,355,387,430,454],difficult:[218,282,370,401,478],difficulti:[92,108,302,432],diffract:[],diffus:[],digit:[2,3,194,339,422],dih_table1:188,dih_table2:188,dihedr:[],dihedral_coeff:[],dihedral_cosineshift:27,dihedral_styl:[],dihedralcoeff:3,dihedraltyp:216,dihydrid:395,dij:302,dilat:[],dim1:3,dim2:3,dim:[3,59,71,145,149,150,151,154,155,156,157,158,160,168,190,210,220,237,332,358,419,472,494,495,496],dimdim:495,dimems:281,dimens:[],dimensinon:71,dimension:[3,39,92,114,120,142,145,148,149,150,151,154,155,156,157,158,160,167,189,206,210,254,281,326,358,361,365,430,469,479],dimensionless:[106,123,124,126,129,131,133,138,142,326,356,441,461],dimentionless:137,dimer:[6,299,419],dimgrai:194,dimstr:[41,214],dinola:[286,317],dintel_offload_noaffin:16,dipol:[],dipolar:[4,29,40,191,316,490],dir1:480,dir2:480,dir:[1,3,4,8,9,11,12,253,280,289,313,430,432,433,467,480,495],dirac:142,direc:430,direct:[],directli:[3,6,8,9,11,12,87,115,142,144,191,192,193,200,226,233,237,242,281,300,318,330,332,333,334,335,358,362,370,371,372,378,380,381,387,390,393,395,407,411,424,427,435,449,467,479,480,481,487,495],directoi:14,directori:[0,1,2,3,4,6,7,8,9,11,12,13,14,15,16,17,60,195,219,238,284,290,293,310,314,323,324,365,369,371,372,377,384,386,387,393,394,396,403,404,415,419,420,421,422,426,430,431,432,433,440,441,451,453,454,455,458,467,469,470,471,480,495],disabl:[3,12,16,326,406,467,482,495],disadvantag:[6,214],disallow:[191,220,255],disappear:471,discard:[2,3,41,71,208,210,214,327,335,466,471,472],discontinu:[9,188,363,413],discourag:419,discov:[13,327],discret:[6,8,40,42,193,194,239,242,376],discuss:[],disk:[6,84,85,92,161,189,221,231,285,467],disloc:[70,422],disord:[39,70,422],disp:[],dispar:434,disperion:[390,411],dispers:[3,6,7,9,166,281,355,356,381,390,411,416,424,433,452,458],displac:[],displace_atom:[],displace_box:59,displacemet:472,displai:[11,13,22,37,44,55,176,187,191,193,341,350,384,450],dispters:3,disregard:422,dissip:[6,232,239,281,323,324,379,391,399,416,417,450],dissolut:215,dist:[6,69,91,110,119,191,282,298,392,449,464,496],distanc:[],distinct:[6,224,296,355,434],distinguish:[6,86,142,245,376,395,468],distort:[166,371],distrbut:371,distribut:[],distro:[113,384,429,430],ditto:[8,12,14,15,16,17,18,42,117,216,462,467],div:8,divd:119,diverg:[3,12,39,299,324,471,490,497],divid:[3,6,16,41,91,114,119,128,130,143,165,166,176,187,194,206,207,209,214,220,280,322,329,334,355,363,365,396,433,440,458,478,486,495],divis:[6,242,377,405,415,466,487,495],dl_poli:[6,7],dlambda:162,dlammps_async_imd:236,dlammps_bigbig:[12,39],dlammps_ffmpeg:[3,12,193],dlammps_gzip:[3,12,191,193,325,469,470,474],dlammps_jpeg:[3,12,193],dlammps_longlong_to_long:12,dlammps_memalign:[12,16],dlammps_png:[3,12,193],dlammps_smallbig:12,dlammps_smallsmal:12,dlammps_xdr:[12,191],dlen:479,dlmp_intel_offload:[12,16],dlo:[59,190,220,285],dlopen:6,dlvo:[7,385,461],dm_lb:242,dmax:[314,361],dna:7,doc:[0,1,2,3,4,6,7,8,9,11,12,13,14,15,16,17,18,22,37,40,42,55,57,59,63,66,68,75,87,90,94,103,105,106,107,109,111,113,114,116,119,121,143,146,147,148,161,163,165,168,169,170,176,187,190,191,192,193,194,195,197,198,199,204,205,206,207,208,209,210,211,212,221,231,239,240,250,255,256,261,262,263,267,274,275,276,277,278,285,288,299,311,314,317,318,319,328,332,335,337,339,341,350,354,363,364,365,370,371,372,375,376,384,386,387,393,394,396,401,402,404,405,419,420,421,424,426,429,430,431,441,450,451,453,455,457,458,467,469,470,471,472,474,477,478,479,486,487,495,496,497,498],docuement:434,dodd:[42,376],dodgerblu:194,doe:[0,1,2,3,5,6,7,8,9,11,12,14,15,16,17,18,33,38,39,41,42,50,54,56,59,62,63,67,70,71,72,87,88,91,105,112,118,119,120,144,146,148,150,151,156,158,162,167,168,169,170,172,174,176,181,187,188,190,191,192,193,194,197,203,204,206,210,213,214,216,217,218,220,224,226,228,231,232,235,237,239,240,242,245,251,255,256,257,258,259,261,262,263,274,275,276,277,278,286,287,288,292,294,297,299,314,317,319,321,322,326,329,330,331,334,335,336,337,342,343,344,346,347,349,354,355,356,357,358,364,365,366,371,372,373,374,375,376,377,379,381,382,383,385,386,387,388,390,391,392,393,394,395,397,398,399,400,402,403,404,405,406,409,410,412,413,414,416,417,419,420,421,422,424,430,431,432,433,434,436,437,438,439,440,441,442,443,444,445,446,447,448,449,451,452,453,454,455,456,457,458,460,461,462,464,465,466,467,469,470,471,472,473,476,477,479,480,481,482,483,486,487,490,495,499],doegenomestolif:7,doesn:[3,7,8,12,168,191,204,210,211,311,364,366,370,372,386,394,404,432,433,451,453,454,455,458,469,471],dof:[3,8,114,146,147,148,161,206,299,496],dof_per_atom:[148,206],dof_per_chunk:[148,206],doff:[364,469],doi:[6,219],domain:[3,6,7,12,13,18,39,41,42,58,61,62,71,120,157,167,170,190,192,193,194,197,204,214,218,220,221,235,238,242,255,256,282,294,299,326,331,332,355,356,365,370,392,424,464,466,469,473,486],domin:[1,395,483],don:[0,8,11,12,13,118,171,200,226,240,288,335,419,440,467,469],donadio:318,done:[1,3,6,7,8,12,14,15,16,17,18,38,39,41,56,59,62,71,162,165,168,171,188,191,193,194,203,204,206,208,209,210,211,212,214,215,216,217,218,220,221,229,231,236,237,239,240,247,255,261,262,263,274,275,276,278,279,281,282,283,285,2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,208,209,212,213,214,218,220,221,226,231,232,234,235,237,239,240,242,245,246,252,253,260,271,280,282,285,287,289,290,291,294,296,298,299,301,303,308,310,317,318,319,322,323,324,326,328,329,331,334,336,337,339,354,358,363,365,366,367,369,370,386,391,397,398,401,405,416,422,423,430,432,433,434,436,437,438,440,441,442,452,457,458,462,465,466,467,469,471,472,476,477,480,483,485,487,495,496],equat:[3,6,7,8,9,91,108,114,120,167,176,187,197,218,224,225,233,239,240,242,245,253,254,255,256,260,276,280,282,289,290,294,302,314,322,326,329,331,332,334,336,349,355,356,385,390,391,395,396,399,404,416,417,419,424,434,437,439,444,445,447,448,462,490],equi:256,equidist:254,equil:[3,290,359,476,499],equilater:479,equilibr:[3,4,5,6,7,9,59,91,168,197,204,207,217,218,231,253,255,256,276,277,289,290,291,292,322,323,324,329,386,387,432,433,465,479],equilibria:329,equilibribum:[215,216],equilibrium:[1,3,4,6,7,21,24,26,27,28,29,32,35,36,38,43,47,48,49,51,53,56,59,151,152,175,177,218,220,231,232,233,240,242,255,260,276,289,290,294,298,302,303,311,314,321,322,324,329,340,342,346,349,386,419,426,440,490],equilibrium_angl:8,equilibrium_dist:8,equilibrium_start:203,equival:[6,12,13,29,59,61,126,127,135,140,166,170,194,209,212,218,220,231,239,255,276,286,298,299,334,391,395,440,453,455,469,472,477,478,487,490],equlibrium:6,equliibr:[290,292],er3:167,eradiu:[40,115,395,469],eras:[301,323],erat:[220,417],erc:387,erfc:[387,407,424],erforc:115,erg:494,erhart:[204,393,453,455],ermscal:373,ernst:9,eror:3,eros:419,erose_form:419,erot:[],errata:[453,455],erratum:331,erron:3,error:[],erta:399,ervel:[115,469],escap:[221,490],especi:[8,11,16,156,168,197,204,214,231,289,294,297,298,370,466],espresso:[9,293],essenti:[8,11,12,27,88,130,149,150,151,154,155,156,157,158,160,177,207,260,281,330,356,372,387,407,455,474,487],essex:29,establish:[87,235],estim:[1,3,6,10,12,38,41,56,91,143,203,214,225,253,314,321,355,356,361,424,433,452,483,487],esu:494,esub:419,eta:[6,242,255,289,290,292,330,394,396,398,430,454,458,494],eta_dot:255,eta_ij:430,eta_ji:396,etag:[40,469],etail:487,etap:255,etap_dot:255,etc:[1,2,3,6,7,8,9,10,11,12,13,15,16,39,40,42,54,61,68,89,90,91,95,111,112,115,117,143,145,148,149,150,151,152,154,155,156,157,158,160,162,168,170,171,172,181,191,193,194,197,198,203,204,205,206,209,210,211,212,215,216,220,221,229,231,232,239,255,285,296,300,326,327,335,339,354,355,363,364,365,366,368,393,394,402,415,417,422,428,432,433,451,453,455,458,464,467,469,470,471,476,478,479,483,485,486,487,488,490,494,495,497,499],ethernet:18,etol:[363,365,464,483],etot0:289,etot:[6,95,97,98,112,143,154,194,224,240,253,289,486,487],eu2:167,eu3:167,euler:[363,365],eulerian:203,euqat:443,europhi:242,ev_tal:8,evalu:[2,3,9,11,12,38,56,71,87,88,91,109,119,142,144,148,158,166,168,190,191,193,194,198,199,200,201,203,205,206,207,208,209,210,211,212,213,220,226,232,234,235,237,238,239,240,281,287,290,301,304,308,317,318,319,328,331,334,336,337,339,355,356,361,363,370,422,424,430,436,438,440,452,464,465,467,471,472,474,476,477,478,479,483,485,487,495,496],evalut:[339,467],evan:[156,276],evanseck:[6,20,174,382,481],evapor:[],evaul:[8,363],evdwl:[109,432,433,487],even:[3,6,8,12,15,17,18,34,39,41,52,57,59,61,63,70,71,121,166,169,170,184,188,191,194,197,198,199,204,205,206,209,210,211,212,214,215,216,218,220,221,224,237,240,253,255,256,281,285,294,296,299,300,310,314,322,326,329,331,335,337,348,355,361,363,365,370,375,395,396,399,402,405,424,434,458,459,469,470,472,474,475,476,478,479,481,484,486,487,488,490,499],evenli:[3,41,143,188,214,242,405,459],event:[],eventu:[3,6,12,15,170,290,483],ever:[54,56,238,314],evera:[385,398,434,450],everi:[0,1,2,3,6,8,9,11,12,15,16,39,41,71,72,91,115,121,130,156,171,191,192,193,194,195,197,198,199,200,203,204,205,206,207,208,209,210,211,212,213,214,215,216,217,218,220,221,225,228,229,231,233,235,236,237,242,243,251,255,256,260,279,280,281,285,286,287,288,289,290,291,292,294,296,297,299,300,302,303,314,316,317,318,319,320,321,322,325,326,327,328,329,337,339,354,356,365,366,367,370,391,392,402,415,432,433,440,446,463,464,465,469,471,473,474,476,477,478,483,484,485,487,495,499],everyth:[8,109],everywher:[118,409],eviri:395,evolut:[233,242,282,464],evolv:[242,282,327],ewald:[2,3,5,6,7,8,12,88,112,120,143,327,355,356,363,378,380,381,387,390,395,407,411,427,435,450,452],ewald_disp:390,ewalddisp:3,exact:[22,41,44,71,124,162,171,176,214,217,232,233,239,240,241,285,294,295,314,326,341,355,384,471,476,483,495,497,499],exactli:[3,6,12,14,17,38,41,42,56,59,71,72,91,118,146,152,159,168,188,198,199,209,214,220,225,232,239,240,241,256,268,269,277,281,289,314,319,320,333,370,384,391,393,399,402,416,424,452,471,472,479,483,495],exager:490,examin:[6,8,9,17,217,281],examp:[467,495],exampl:[],exce:[3,6,16,17,18,41,58,71,170,205,206,209,210,211,212,214,218,220,225,228,255,281,296,300,305,306,314,363,370,469,495],exceed:[3,41,59,214,220,255,314,477],excel:395,except:[1,2,5,6,8,9,11,14,20,21,22,23,24,25,26,27,28,29,30,31,32,35,37,38,40,41,43,44,45,46,47,48,49,51,53,54,55,56,59,60,63,71,89,90,110,111,114,119,143,145,146,147,148,149,150,151,152,154,155,156,157,158,159,160,161,168,172,174,175,176,177,178,179,180,182,183,185,186,187,188,190,191,194,197,200,206,207,209,213,214,218,220,227,230,231,234,237,239,241,255,256,257,258,259,260,261,262,263,264,265,268,269,272,274,275,276,277,278,282,291,292,299,301,302,311,314,317,319,320,326,330,334,337,339,340,341,342,343,345,346,349,350,351,355,356,358,360,364,365,366,368,369,370,371,372,374,378,379,380,381,382,383,384,385,386,387,389,390,391,393,394,395,396,397,398,399,400,401,402,407,408,409,410,411,412,413,414,415,416,417,420,425,426,427,429,432,433,434,435,442,450,451,452,453,454,455,458,460,461,462,464,466,467,469,471,472,474,477,478,479,480,481,483,487,490,494,495,496,498],excess:[208,395],exchang:[2,3,6,8,9,61,62,197,203,204,231,239,291,299,322,326,329,355,370,395,484],exchange:355,excit:[9,395],exclud:[3,6,9,12,16,17,63,71,114,142,148,155,156,172,191,206,210,215,216,243,251,284,297,299,321,332,337,363,364,366,379,399,402,405,416,417,424,449,481],exclus:[1,3,9,12,16,87,370,386,422,424,478,488],excurs:[255,464],exectubl:12,execut:[1,2,3,4,6,8,11,12,17,60,169,193,236,293,339,354,357,369,465,467,477,480,483,495],exempl:440,exemplari:232,exemplifi:395,exert:[6,237,240,294,333,334,335,356],exhaust:[203,369,495],exhibit:[92,255,362,395,478],exist:[3,6,7,8,11,12,13,16,37,55,59,68,70,124,168,169,187,192,193,194,197,202,213,216,218,221,231,284,285,287,337,340,342,343,344,346,350,359,364,370,402,432,449,459,465,467,469,470,471,480,481,482,495,496,497],exit:[2,3,11,12,41,57,191,214,354,369,467,468,477,486,495],exlanatori:3,exp:[],expand:[],expans:[12,142,191,480,495],expect:[1,3,8,12,13,14,15,16,17,18,19,41,42,71,103,149,160,166,188,214,226,231,233,252,280,286,288,289,294,299,337,356,366,384,419,422,424,464,467,469,471,474,478,483,495],expens:[6,10,71,194,280,284,299,326,337,355,356,366,370,467],experi:[6,13,15,17,213,221,236,245,254,286,298,299,361,365,391,424,478,483],experienc:[6,12,244,245],experiment:[231,355,370,483],expert:12,expertis:7,explain:[1,3,6,8,9,11,12,16,18,41,59,63,65,68,69,71,72,73,76,77,79,86,93,148,156,188,191,193,194,197,206,207,212,214,216,218,220,255,280,288,299,311,337,339,354,355,358,364,365,369,375,393,405,440,442,457,467,470,471,474,476,479,490,495,499],explan:[3,6,59,115,142,191,206,254,280,402,463,466,467,469,478],explanatori:[3,8,119,191,205,206,209,210,211,299,364,466,495],explantori:[3,295],explic:423,explicit:[6,9,11,22,44,77,87,115,118,162,176,198,199,220,305,306,341,360,372,373,377,382,384,393,395,406,416,456,463,466,470,473],explicitli:[3,6,8,12,14,15,16,17,18,19,20,21,23,24,25,26,27,28,29,30,31,32,35,38,40,43,45,46,47,48,49,51,53,54,56,71,111,114,145,155,158,166,168,174,175,177,178,179,180,182,183,185,186,188,191,194,200,210,213,220,227,230,232,234,239,255,257,258,259,260,261,262,263,264,265,272,274,275,276,278,288,289,291,299,301,302,317,319,320,326,330,334,340,342,343,345,346,349,351,364,370,371,372,374,378,379,380,381,382,383,384,385,386,387,388,390,391,392,393,394,396,397,398,399,400,401,402,406,407,408,409,410,411,412,413,414,415,416,420,422,424,425,426,427,429,434,435,442,443,444,445,446,447,448,450,451,452,453,454,455,456,458,460,461,462,469,471,472,478,479,481,482,488,490],explictli:[16,482],exploit:[9,15,17,282],explor:[120,167],expon:[3,290,292,393,398,401,415,423,435],exponenti:[87,430,451,458,462,483,495],expos:11,exposit:[203,391,392],express:[6,142,154,168,198,199,218,252,280,290,326,332,339,377,393,395,409,419,440,441,450,495],expressiont:377,extend:[],extens:[3,6,9,17,44,45,46,53,55,63,82,83,84,87,88,91,95,98,99,109,111,119,121,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,197,200,201,204,212,213,219,222,226,229,230,231,233,234,235,237,239,241,253,255,260,269,280,281,297,298,299,301,303,308,311,313,317,318,319,320,321,323,324,326,328,331,335,336,398,419,422,433,434,441,486,487],extent:[1,3,41,42,45,57,71,166,170,191,202,210,214,237,333,336,355,358,372,436,438,452,466,469,472],exterior:[3,6,166,335],extern:[],extra:[3,6,8,12,16,17,40,41,46,61,71,103,111,112,114,120,143,145,146,147,149,151,154,155,156,157,158,160,161,167,168,169,170,174,194,209,214,216,255,287,288,289,299,314,363,364,367,368,390,399,402,405,419,424,466,467,469,472,481,490,495],extract:[3,6,11,13,36,63,87,109,117,119,121,198,199,292,365,387,396,419,441,467,474,486],extract_atom:11,extract_comput:[11,467],extract_fix:11,extract_glob:11,extract_vari:11,extramak:[12,15],extrapol:1,extrem:[1,3,6,17,58,193,208,218,220,255,324,395,454,490],extrema:415,extrins:203,f77:[5,7,12],f90:[5,7,12],f_1:6,f_5:[164,328],f_a:[453,454,455],f_ave:119,f_c:454,f_f:455,f_fix_id:289,f_harm:324,f_i:[29,430],f_id:[6,71,119,121,191,197,205,206,207,208,209,210,211,212,250,316,328,487,495],f_ij:430,f_indent:212,f_int:323,f_j:29,f_jj:91,f_k:430,f_langevin:326,f_max:[289,294],f_msst:253,f_r:[240,453,454,455],f_sigma:377,f_solid:324,f_ss:6,f_temp:[],face:[3,6,57,59,71,156,166,170,202,210,211,331,333,334,335,336,358,398,419,434,469,472],face_threshold:166,facet:166,facil:[0,12],facilit:[6,13,42],fact:[6,8,16,233,285,314,324,399,440,481],factor:[1,3,6,12,18,24,28,32,35,36,39,41,46,47,57,58,59,72,87,91,103,110,117,118,120,142,162,167,170,174,185,190,191,193,194,198,199,207,214,218,220,221,231,236,239,241,242,253,255,256,260,282,286,290,298,302,304,306,314,318,322,329,330,331,335,346,356,358,364,370,372,373,377,378,380,382,387,388,389,391,395,399,402,406,407,419,422,424,426,427,433,435,442,451,456,466,469,472,473,478,481,483,484,487,490,494,495],factori:[3,467],factoriz:355,fail:[3,11,12,59,172,218,221,355,363,365,389,433,467],failur:[123,437,468,495],fairli:[11,424,478,483],faken:73,falcon:236,fall:[3,6,194,209,285,467,495],fals:[86,337,339,440,495],fame:8,famili:[458,466],familiar:[0,11],fan:430,far:[3,6,12,17,57,59,61,86,191,194,195,214,215,216,218,221,255,280,298,299,314,331,342,346,361,365,366,457,467,469,474,487],farago:239,farrel:[453,455],farther:191,fashion:[6,8,41,71,168,194,197,198,199,204,210,214,216,221,231,233,237,252,253,255,257,258,259,260,261,262,263,271,274,275,276,277,278,288,289,291,299,303,307,313,316,324,326,330,331,332,334,336,365,402,416,472,481,495,498],fasolino:404,fast:[6,7,9,12,13,17,39,191,266,289,327,355,356,379,416,417,422,450,452,471,476,478,487,496,499],faster:[1,6,9,10,11,12,14,15,17,18,20,21,23,24,25,26,27,28,29,30,31,32,35,38,40,41,43,45,46,47,48,49,51,53,54,56,61,63,106,111,114,145,155,174,175,177,178,179,180,182,183,185,186,188,191,194,200,213,214,220,227,230,234,238,239,255,257,258,259,260,261,262,263,264,265,272,274,275,276,278,286,290,291,299,301,302,314,317,319,321,323,326,330,334,340,342,343,345,346,349,351,355,356,367,368,370,371,372,374,377,378,379,380,381,382,383,384,385,386,387,390,391,393,394,396,397,398,399,400,401,402,407,408,409,410,411,412,413,414,415,416,420,425,426,427,429,434,435,442,450,451,452,453,454,455,458,460,461,462,464,472,478,482,490],fastest:[1,6,14,17,156,210,326,327,370,466],fatal:[3,486],fault:[70,433],faulti:12,fava:398,favor:217,favorit:7,fbmc:321,fcc:[],fcm:[271,495],fdirect:224,fdotr:403,fdti:87,fe2:167,fe3:167,fe_md_boundari:203,featu:8,featur:[],fecr:393,feedback:[7,236],feel:[7,236,237,245,280,335,337,365,424],felling:421,felt:335,femtosecond:494,fene:[],fennel:[387,407],fep:[],ferguson:[6,174,481],fermi:[1,12,15,154,370,455],fermion:[9,395],fernando:418,ferrand:[9,13],few:[1,3,4,5,6,7,9,10,11,12,13,14,18,39,63,195,205,206,207,209,210,211,212,240,255,285,288,290,302,328,355,363,364,365,372,440,466,469,474,478,480,488,495,497],fewer:[1,3,11,15,16,61,245,478],fewest:3,fextern:229,feynman:282,fff:467,ffield:[386,396,432,433,440],ffmpeg:[3,12,193],ffplai:193,fft:[1,3,7,12,14,15,88,111,112,143,281,355,356,478],fft_inc:[12,356],fft_lib:12,fft_path:12,fftbench:[355,488],fftw2:12,fftw3:12,fftw:[11,12],fhg:[7,9],ficiti:449,fictiti:[6,200,201,226,229,233,282,298,387,407,411,449],field1:[470,474],field2:470,field:[],fifth:[311,426],figur:[1,3,8,11,12,289,466,467],fij:390,file0:280,file1:[11,13,280,325,339,364,474,476,480],file2:[11,13,325,339,364,474,476,480],file:[],file_from:192,filen:364,filenam:[3,12,13,38,41,56,188,191,193,194,195,203,206,207,208,209,210,211,212,214,219,280,284,287,290,291,292,295,296,299,300,325,326,352,353,354,364,365,371,372,377,387,393,394,396,404,419,420,421,426,430,431,432,433,440,441,451,452,453,454,455,458,465,466,467,470,471,476,480,487,495,497,498,499],filennam:476,filep:[3,191,194,471,476,499],filepo:296,fill:[7,9,168,193,285,326,358,366,377,422,433,472],filter:[194,203],final_integr:8,final_integrate_respa:8,finchham:[6,150,389],find:[0,3,4,6,7,8,11,12,13,14,16,38,39,56,61,71,73,87,119,171,188,195,204,217,218,228,231,254,280,285,286,294,298,361,363,365,366,387,402,407,411,419,440,450,452,490,495],find_custom:8,fine:[16,17,172,200,226,324,366,370,495],finer:[142,168,495],finest:355,finger:[168,190,252,472],finish:[6,11,41,214,339,352,354,355,367,369,370,457,474,495,496],finit:[],finni:[7,393,450],finvers:224,fiorin:[9,219],fire:[],firebrick:194,first:[0,1,2,3,5,6,8,9,11,12,14,15,16,17,21,38,39,41,42,45,46,54,56,57,59,61,62,71,81,88,91,104,105,106,108,114,118,119,129,132,135,136,140,143,153,156,162,164,166,167,169,170,171,175,188,191,192,193,194,195,197,198,206,207,209,210,211,212,214,217,220,231,232,237,242,252,253,254,255,280,282,287,288,289,291,296,299,302,303,311,312,314,315,316,323,324,325,326,328,332,337,339,340,347,358,363,364,365,366,369,370,371,372,375,377,378,380,382,384,386,387,393,395,396,399,400,402,403,404,405,406,407,411,416,417,419,421,422,424,426,430,432,433,440,441,449,451,452,453,454,455,458,462,464,465,466,467,469,470,471,474,476,478,481,482,483,486,487,490,495,496,497,499],fischer:[6,9,19,20,174,382,481],fit:[3,6,9,12,38,56,188,298,314,372,377,404,419,424,445,452,454,477,495],five:[73,154,289,364,377,420,469,483],fix:[],fix_adapt:[162,199,415],fix_atom_swap:[],fix_bal:62,fix_deposit:[3,204,285],fix_evapor:204,fix_flux:203,fix_gcmc:[204,364],fix_gl:233,fix_gld:233,fix_grav:285,fix_id:[3,218,253,255,257,258,259,260,261,262,263,286,289],fix_modifi:[],fix_mov:[190,332],fix_nh:8,fix_npt:233,fix_nvt:[204,231],fix_poem:[3,6],fix_pour:[3,221],fix_qbmsst:9,fix_qeq:[3,386],fix_rattl:302,fix_reax_bond:432,fix_rigid:[245,375],fix_saed_vtk:300,fix_setforc:8,fix_shak:302,fix_srd:3,fix_styl:260,fix_temp_rescal:320,fixedpoint:[218,255],fixextern:229,fixid:203,fji:390,flag1:[223,368],flag2:[223,368],flag:[3,8,11,12,14,15,16,17,40,66,74,75,81,86,89,90,94,104,105,107,120,163,167,171,191,193,194,195,212,217,219,223,236,239,243,245,251,252,281,288,299,311,313,314,321,325,334,337,353,356,364,368,369,370,372,401,406,419,422,449,464,466,467,469,470,471,473,474,475,479,495],flag_buck:381,flag_coul:[381,390,411],flag_lj:[390,411],flagfld:[379,416,417],flaghi:[3,379,416,417],flaglog:[379,416,417],flagn:223,flagvf:[379,416,417],flat:[6,326,331,332,336],flavor:[2,7,12],fld:[9,331,379,416,417],flen:373,flex_press:373,flexibl:[3,6,8,169,193,206,210,219,233,256,322,329,395,454,487],flip:[3,6,220,255,333,334],floor:495,flop:12,floralwhit:194,flow:[],fluctuat:[6,64,87,218,231,232,239,242,255,260,280,281,324,326,349],fluid:[],fluid_veloc:246,flush:[3,194,486],flux:[],flv:193,fly:[7,9,12,41,193,197,203,208,221,224,299,302,327,377,422,487,490],fmackai:9,fmag:222,fmass:282,fmax:[363,487],fmomentum:224,fmsec:[2,194,239,240,252,255,286,299,317,318,478,489,494,496],fname:354,fno:[12,16],fnorm:[363,487],fnpt:224,fnvt:224,foce:402,fock:373,focu:302,fogarti:[9,292,433],foil:[142,280,441],fold:[312,478],folk:7,follow:[0,1,2,3,4,6,7,8,9,11,12,13,14,15,16,17,18,19,20,23,24,25,26,27,28,29,30,31,32,35,36,38,41,42,43,45,46,47,48,49,51,53,54,56,59,63,64,70,71,73,91,92,97,98,108,115,118,119,121,142,143,146,147,148,154,156,161,164,166,168,169,174,177,178,179,180,182,183,185,186,188,191,192,193,194,197,203,204,205,206,207,208,209,210,211,212,214,219,220,221,224,225,229,231,232,233,236,238,239,240,242,245,253,255,260,261,262,263,274,275,276,278,281,282,284,287,288,289,290,292,294,296,298,299,300,302,316,317,318,319,322,323,324,325,326,328,329,337,338,342,343,344,345,346,349,351,353,358,360,363,364,365,370,371,372,373,374,375,376,377,378,379,380,381,382,383,385,386,387,388,389,390,391,392,393,395,396,397,398,399,400,401,402,403,404,405,406,407,408,409,410,411,412,413,414,415,416,417,418,419,420,421,423,424,425,426,427,429,430,431,432,433,434,435,437,439,440,441,442,443,444,445,446,447,448,449,451,452,453,454,455,456,457,458,460,461,462,464,466,467,469,470,472,474,476,477,478,481,483,484,485,490,495,496,498],foo:[4,8,11,12,191,193,229,467,480,495],foot:6,footprint:[12,370],fopenmp:[12,16,18],forc:[],force_uvm:17,forceatom:245,forcefield:[298,401],forcegroup:242,forcezero:361,ford:390,forestgreen:194,forev:71,forget:[240,490],forgiv:255,fork:[12,191],form:[2,3,6,8,12,19,22,44,54,63,66,74,75,77,81,87,89,90,92,94,104,105,107,118,142,143,162,163,172,176,194,197,198,199,216,232,233,239,241,245,252,276,281,292,294,298,299,326,331,335,340,341,344,349,360,362,364,365,372,373,377,384,393,395,397,401,402,406,418,419,421,422,426,427,430,432,433,434,440,441,442,450,452,453,454,455,461,463,466,467,469,474,479,486,490,495],formal:[6,78,80,91,232,233,239,255,282,314,322,440],format:[2,3,6,7,8,9,12,13,22,38,41,44,56,68,77,176,188,191,192,193,194,195,206,209,210,211,212,214,216,281,284,288,290,292,295,299,300,310,325,326,337,338,341,360,364,365,371,372,377,384,393,396,406,419,421,431,432,433,435,441,452,458,459,466,467,469,470,471,474,485,486,487,495,497],former:[6,12,16,39,41,194,214,326,330,377,379,475,481,495],formerli:[7,13],formul:[1,40,64,143,200,226,239,255,276,290,292,298,302,325,355,372,377,393,395,398,419,429],formula:[2,3,6,7,13,21,22,37,44,54,55,70,73,87,89,90,91,95,97,98,107,114,120,143,145,146,147,148,149,150,151,152,154,155,156,157,158,159,160,161,167,168,173,175,176,187,190,191,198,199,200,201,206,207,208,209,212,213,220,226,234,235,237,239,240,252,280,281,287,296,301,308,312,314,317,318,319,328,331,334,336,337,339,340,341,343,350,358,364,372,373,375,377,382,383,384,385,390,391,393,394,398,399,400,401,403,406,407,409,410,411,413,414,416,417,419,423,424,425,434,435,442,450,451,453,454,455,458,460,461,465,469,472,479,486,487,494,495,496],forth:[1,6,11,12,13,14,15,369,467,472,476],fortran:[3,6,9,11,12,13,229,393,402,419,432,433],fortun:8,forward:[3,8,87,354,365,370],foster:[377,429,430],foul:171,found:[3,6,9,12,73,162,191,217,219,231,236,242,281,321,327,339,354,366,384,387,390,464,470,471,486],four:[6,11,54,81,104,105,142,164,253,326,349,364,365,422,464],fourier:[],fourth:[6,106,298,311,321,382,426,440],fox:[6,120,174,448,481],fphi:[38,56,452],fpic:12,fplo:[38,56,452],fprime:452,fqdn:238,fqq:390,frac:[],fraction:[1,3,6,8,12,16,39,41,80,111,143,171,190,193,194,204,215,216,217,218,253,285,289,296,297,314,319,320,358,365,370,377,379,399,416,417,474,479],fragment:[42,236,296],fraig:[42,376],frame:[83,142,194,203,253,289,333,398],framer:[193,194],framework:[5,233,371,441],franc:9,fraunhof:9,free:[5,6,7,9,13,29,60,63,70,87,162,199,280,314,323,324,325,326,362,365,373,395,415,422,430,461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recomput:[103,130,172,225,303,392,481],reconstruct:[3,219,440],record:[195,219,303],recov:[218,255],rectangl:[41,214,358],rectangular:[7,41,62,170,214,231,358,469,471,473],rectilinear:[120,167],rector:53,recurs:[41,214,377,457],recust:41,recv:466,red:[2,10,193,194,217,282],redefin:[3,471,477,495],redirect:12,redo:12,reduc:[],reduct:[18,19,119,120,167,253,289,355],redund:396,ree:445,reed:[253,289],rees:[7,9,13],ref:[323,324,362],refactor:6,refer:[],referenc:[3,6,12,63,68,71,116,191,197,207,212,231,288,328,356,387,401,426,434,467,487,495],reflect:[],reformat:7,refresh:203,reg:472,regard:[6,59,252,302,307,429,433],regardless:[15,71,168,171,190,209,210,220,239,255,257,258,259,261,262,263,286,299,308,314,370,466,472,479],regim:[6,322,329,388,478],region:[],region_spher:8,region_styl:335,regist:[8,118,144,310,432,433],regoin:6,regress:495,regspher:168,regstrip:337,regul:6,regular:[1,3,9,41,62,88,166,170,191,193,204,214,231,326,356,388,405,466,469,471,473],reigon:495,reinhardt:[323,324],reject:[168,217,432,484],rel:[1,6,14,27,36,41,59,71,92,104,124,132,142,146,150,151,153,168,177,194,197,204,210,214,220,221,224,231,237,240,251,252,276,280,285,294,296,297,303,311,314,316,321,322,326,333,337,355,356,363,395,398,399,416,417,419,434,461,470,478,483,487,490,496],relat:[],relatic:[],relationship:[6,290,339,355,440,461,490,495],relax:[],releas:[0,5,7,8,13,215],relect:[3,424],reles:42,relev:[2,6,12,41,78,80,113,130,168,172,194,198,199,202,203,204,205,206,207,208,209,210,211,212,213,214,215,216,220,221,222,225,227,228,230,231,232,235,236,242,243,244,246,247,248,249,251,252,254,264,265,266,267,268,269,270,271,272,273,279,283,284,285,287,288,291,293,295,296,297,300,301,302,303,308,312,314,315,316,321,322,325,326,327,328,329,330,331,332,333,334,336,337,355,363,373,374,379,385,387,388,390,391,392,395,397,398,399,400,401,406,408,409,410,412,413,414,416,417,424,425,429,434,442,449,452,460,461,462,466,482,496],reli:[3,12,291,395,433,462,469,479],reloc:12,remain:[7,12,33,37,41,50,55,59,71,87,105,148,149,150,151,155,156,157,158,160,171,181,187,188,191,198,199,204,206,207,210,211,218,220,239,240,247,255,256,261,262,263,274,275,276,278,283,284,306,314,317,318,319,325,326,337,339,347,350,364,377,395,402,415,422,424,450,464,469,470,474,479,481,483,487,490,495,496],remaina:377,remaind:[168,191,221,285,314,327,455,469],remap:[3,6,12,59,61,71,151,168,190,210,220,237,252,276,355,469,470,471],remedi:[6,490],rememb:2,remov:[2,3,6,8,9,13,54,71,72,77,92,108,116,118,142,146,147,148,149,150,151,155,156,157,158,160,161,168,171,172,197,206,210,215,228,239,240,245,251,253,255,261,262,263,274,275,276,278,284,290,299,300,302,314,317,318,319,321,337,355,365,390,417,422,469,472,480,481,495,496],remove_bia:8,remove_bias_al:8,remove_molecul:203,remove_sourc:203,remove_speci:203,ren:167,renam:[12,338,480],render:[12,13,191,193,194],rendon:[255,256],reneighbor:[3,8,12,39,57,71,210,214,231,314,327,337,391,486,487],renssela:284,renumb:71,reorder:[3,12,39,466],repeat:[2,6,193,194,210,217,218,231,307,358,377,453,455,457,464,483],repeatedli:2,repel:237,repes:191,replac:[2,3,6,11,12,41,63,89,90,119,145,146,147,148,149,150,151,154,155,156,157,158,160,161,191,193,194,195,206,207,209,210,211,212,214,217,221,239,260,287,294,296,387,409,470,471,476,477,487,495,496,497,499],replic:[],replica:[],replica_fil:12,report:[],repositori:[7,12,403,431,432,433],reprens:326,repres:[1,3,6,8,9,12,15,40,41,42,59,67,71,90,115,118,180,188,191,193,206,207,208,209,210,211,212,218,224,232,234,239,242,255,282,284,286,294,299,300,303,311,326,328,335,356,365,371,377,398,405,415,416,417,419,420,421,427,430,432,433,456,457,464,466,469,479,481,484,490,495,497],represent:[3,6,8,9,57,59,136,170,191,232,233,282,326,377,395,398,422,434,469,472,490],reprocess:474,reproduc:[3,255,332,387,393,399],repul:419,repuls:[6,7,9,36,40,45,46,110,237,290,331,332,335,372,376,377,385,387,391,395,399,401,415,419,423,440,449,455,458,461,462,479],reqir:[290,292],request:[3,6,8,12,41,104,171,188,191,236,242,297,314,316,353,355,424,432,433,464,474,479,483,495,496,497],requir:[],rerun:[],rescal:[],research:[5,7,242,246,422,464,483],resembl:294,reserv:[12,236,490],reservoir:[91,231,235,239,326],reset:[],reset_atomic_reference_posit:203,reset_dt:8,reset_target:8,reset_tim:203,reset_timestep:[],resid:13,residu:236,residue1:366,resist:[6,236],resolut:[208,440,452],resolv:[218,282,314,417],resort:3,resourc:[7,371,393],respa:[3,16,225,236,255,368,371,372,373,374,375,376,377,378,379,380,381,382,383,385,386,387,388,390,391,392,393,394,395,397,398,399,400,401,402,403,404,405,406,407,408,409,410,411,412,413,414,416,417,418,419,420,421,422,423,425,427,429,431,432,433,434,435,440,441,442,443,444,445,446,447,448,449,451,452,453,454,455,457,458,460,461,462,477,478,489,495],respecifi:422,respect:[1,6,9,10,13,14,15,17,20,21,23,24,25,26,27,28,29,30,31,32,35,38,40,42,43,45,46,47,48,49,51,53,54,56,59,70,71,87,89,97,98,111,114,120,124,145,150,153,155,162,166,167,174,175,177,178,179,180,182,183,185,186,188,193,194,210,211,216,217,218,22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ai:454,sall:[9,440],salmon:194,salt:[388,397,419,469],salter:440,same:[1,2,3,4,6,8,10,11,12,13,14,15,16,17,18,20,21,22,23,24,25,26,27,28,29,30,31,32,33,35,38,39,40,41,43,44,45,46,47,48,49,50,51,53,54,56,57,59,62,63,65,69,71,72,77,79,81,82,84,85,87,88,89,90,91,92,93,95,98,104,105,106,108,110,111,112,114,115,117,118,119,142,143,144,145,146,147,148,149,150,151,154,155,156,157,158,160,161,162,164,166,168,169,170,171,172,174,175,176,177,178,179,180,181,182,183,185,186,188,189,190,191,192,193,194,197,198,199,200,203,204,206,209,210,211,212,213,214,215,216,217,218,220,221,225,226,227,230,231,232,233,234,235,236,237,238,239,240,241,242,245,252,255,257,258,259,260,261,262,263,264,265,272,274,275,276,277,278,280,281,282,284,285,286,289,290,291,292,294,295,296,297,298,299,301,302,303,308,311,313,314,315,316,317,318,319,320,321,322,323,324,325,326,328,329,330,332,333,334,335,337,339,340,341,342,343,345,346,349,351,355,356,358,359,360,364,365,366,367,368,369,370,371,372,374,377,378,379,380,381,382,383,384,385,386,387,388,389,390,391,392,393,394,395,396,397,398,399,400,401,402,403,406,407,408,409,410,411,412,413,414,415,416,417,419,420,423,424,425,426,427,429,430,434,435,440,442,449,450,451,452,453,454,455,458,460,461,462,464,466,467,469,470,471,472,474,477,478,479,480,481,482,483,487,490,494,495,496,498],sampl:[1,2,4,6,9,10,11,12,14,91,104,146,147,161,166,190,193,206,207,210,211,219,221,229,231,233,235,255,256,282,285,294,296,300,311,312,314,318,321,324,336,366,377,392,469,483],sample_frequ:203,san:429,sandia:[0,5,7,9,13,14,17,70,113,396,419,429],sandybrown:194,saniti:[298,366],satellit:[6,150],satifsi:495,satisfi:[3,12,73,120,142,167,218,242,260,302,334,363,366,399,483],satur:388,save:[6,8,12,19,40,59,188,193,208,217,232,233,239,240,241,285,294,326,356,366,368,377,471,474,481],sb3:167,sb5:167,sc3:167,scalabl:[],scalar:[],scale:[0,1,3,4,5,6,9,10,13,18,40,59,63,71,72,91,115,118,119,142,154,162,188,190,191,193,194,197,198,199,203,204,207,218,220,231,235,236,237,239,241,242,253,255,257,258,259,260,261,262,263,282,286,289,290,299,305,306,314,316,318,321,323,324,326,330,337,355,356,358,364,367,371,372,373,388,392,395,399,402,416,417,419,422,429,436,438,456,470,472,474,478,481,483,486,487,495,496],scale_factor:[436,438],scalegamma:242,scalexi:[3,218,255,260],scalexz:[218,255,260],scaleyz:[218,255,260],scan:[194,216,354,470],scatter:[11,120,167],scatter_atom:11,scatter_coord:11,scenario:[6,40,61,217,288,297,314,327,335,366,473,474,478,486],scf:490,schaik:415,schedul:464,schell:454,schemat:217,scheme:[6,9,18,232,233,255,282,294,302,326,355,456],schlitter1:325,schlitter2:325,schlitter:325,schmid:391,schneider:[239,241],schoen:355,schr:490,schroding:395,schroeder:[108,490],schulten:[240,303,356,490],schunk:314,schwen:9,sci:[73,334,386,421,430,440],scienc:[8,203,217,236,303,323,393,420,440,454],scientif:[142,393],scm:11,scratch:[12,41,214],screen:[],screenshot:11,scripe:11,script:[],scripta:67,scsl:12,sdk:[],sea:11,seagreen:194,seamlessli:288,search:[0,2,3,8,12,92,108,169,171,194,195,314,361,362,363,365,367,464,470,471,483,495],seashel:194,sec:[12,489,494],second:[1,3,6,9,10,11,12,16,54,57,59,61,71,88,91,104,106,108,114,135,136,140,143,144,156,162,166,167,169,170,171,190,191,194,197,198,206,207,209,210,211,212,217,231,232,237,252,254,282,296,298,299,302,303,311,312,314,323,324,326,337,355,358,362,363,365,366,370,375,377,378,380,381,386,387,393,395,396,399,400,402,405,406,409,419,424,426,440,451,454,455,456,458,462,464,465,466,467,469,471,476,478,482,483,487,490,494,495,496,497,499],second_mo:440,secondari:[3,180],sectinn:498,section:[0,1,2,3,4,5,6,7,8,9,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,51,53,54,55,56,58,59,63,64,65,66,67,68,69,71,74,75,78,79,80,81,83,86,87,88,89,90,91,93,94,97,98,99,100,101,102,104,105,106,107,109,110,111,113,114,115,116,117,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,144,145,146,147,148,149,151,152,153,154,155,156,157,158,159,160,161,162,163,164,166,167,169,174,175,176,177,178,179,180,181,182,183,185,186,187,188,190,191,192,193,195,197,200,201,202,203,204,206,207,208,209,210,211,212,213,214,215,216,217,219,220,221,223,224,226,227,228,230,231,232,233,234,236,238,239,240,241,242,243,244,245,246,248,249,252,253,254,255,256,257,258,259,260,261,262,263,264,265,266,267,268,270,272,273,274,275,276,277,278,280,281,282,284,285,286,288,289,290,291,292,293,294,295,296,299,301,302,303,304,305,306,307,308,310,314,317,318,319,320,321,322,323,324,325,326,327,329,330,332,333,334,337,338,340,341,342,343,344,345,346,347,349,350,351,356,357,358,360,364,365,367,369,370,371,372,374,375,376,377,378,379,380,381,382,383,384,385,386,387,388,389,390,391,392,393,394,395,396,397,398,399,400,401,402,403,404,405,406,407,408,409,410,411,412,413,414,415,416,417,418,419,420,421,422,424,425,426,427,429,430,431,432,433,434,435,436,437,438,439,440,441,442,443,444,445,446,447,448,449,450,451,452,453,454,455,456,457,458,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Documentation","5. Accelerating LAMMPS performance","3. Commands","12. Errors","7. Example problems","13. Future and history","6. How-to discussions","1. Introduction","10. Modifying & extending LAMMPS","4. Packages","8. Performance & scalability","11. Python interface to LAMMPS","2. Getting Started","9. Additional tools","5.USER-CUDA package","5.GPU package","5.USER-INTEL package","5.KOKKOS package","5.USER-OMP package","5.OPT package","angle_style charmm command","angle_style class2 command","angle_coeff command","angle_style cosine command","angle_style cosine/delta command","angle_style cosine/periodic command","angle_style cosine/shift command","angle_style cosine/shift/exp command","angle_style cosine/squared command","angle_style dipole command","angle_style fourier command","angle_style fourier/simple command","angle_style harmonic command","angle_style hybrid command","angle_style none command","angle_style quartic command","angle_style sdk command","angle_style command","angle_style table command","atom_modify command","atom_style command","balance command","Body particles","bond_style class2 command","bond_coeff command","bond_style fene command","bond_style fene/expand command","bond_style harmonic command","bond_style harmonic/shift command","bond_style harmonic/shift/cut command","bond_style hybrid command","bond_style morse command","bond_style none command","bond_style nonlinear command","bond_style quartic command","bond_style command","bond_style table command","boundary command","box command","change_box command","clear command","comm_modify command","comm_style command","compute command","compute ackland/atom command","compute angle/local command","compute angmom/chunk command","compute basal/atom command","compute body/local command","compute bond/local command","compute centro/atom command","compute chunk/atom command","compute cluster/atom command","compute cna/atom command","compute com command","compute com/chunk command","compute contact/atom command","compute coord/atom command","compute damage/atom command","compute dihedral/local command","compute dilatation/atom command","compute displace/atom command","compute erotate/asphere command","compute erotate/rigid command","compute erotate/sphere command","compute erotate/sphere/atom command","compute event/displace command","compute fep command","compute group/group command","compute gyration command","compute gyration/chunk command","compute heat/flux command","compute hexorder/atom command","compute improper/local command","compute inertia/chunk command","compute ke command","compute ke/atom command","compute ke/atom/eff command","compute ke/eff command","compute ke/rigid command","compute meso/e/atom command","compute meso/rho/atom command","compute meso/t/atom command","compute_modify command","compute msd command","compute msd/chunk command","compute msd/nongauss command","compute omega/chunk command","compute orientorder/atom command","compute pair command","compute pair/local command","compute pe command","compute pe/atom command","compute plasticity/atom command","compute pressure command","compute property/atom command","compute property/chunk command","compute property/local command","compute rdf command","compute reduce command","compute saed command","compute slice command","compute smd/contact/radius command","compute smd/damage command","compute smd/hourglass/error command","compute smd/internal/energy command","compute smd/plastic/strain command","compute smd/plastic/strain/rate command","compute smd/rho command","compute smd/tlsph/defgrad command","compute smd/tlsph/dt command","compute smd/tlsph/num/neighs command","compute smd/tlsph/shape command","compute smd/tlsph/strain command","compute smd/tlsph/strain/rate command","compute smd/tlsph/stress command","compute smd/triangle/mesh/vertices","compute smd/ulsph/num/neighs command","compute smd/ulsph/strain command","compute smd/ulsph/strain/rate command","compute smd/ulsph/stress command","compute smd/vol command","compute sna/atom command","compute stress/atom command","compute force/tally command","compute temp command","compute temp/asphere command","compute temp/body command","compute temp/chunk command","compute temp/com command","compute temp/cs command","compute temp/deform command","compute temp/deform/eff command","compute temp/drude command","compute temp/eff command","compute temp/partial command","compute temp/profile command","compute temp/ramp command","compute temp/region command","compute temp/region/eff command","compute temp/rotate command","compute temp/sphere command","compute ti command","compute torque/chunk command","compute vacf command","compute vcm/chunk command","compute voronoi/atom command","compute xrd command","create_atoms command","create_bonds command","create_box command","delete_atoms command","delete_bonds command","dielectric command","dihedral_style charmm command","dihedral_style class2 command","dihedral_coeff command","dihedral_style cosine/shift/exp command","dihedral_style fourier command","dihedral_style harmonic command","dihedral_style helix command","dihedral_style hybrid command","dihedral_style multi/harmonic command","dihedral_style nharmonic command","dihedral_style none command","dihedral_style opls command","dihedral_style quadratic command","dihedral_style command","dihedral_style table command","dimension command","displace_atoms command","dump command","dump h5md command","dump image command","dump_modify command","dump molfile command","echo command","fix command","fix adapt command","fix adapt/fep command","fix addforce command","fix addtorque command","fix append/atoms command","fix atc command","fix atom/swap command","fix ave/atom command","fix ave/chunk command","fix ave/correlate command","fix ave/correlate/long command","fix ave/histo command","fix ave/spatial command","fix ave/spatial/sphere command","fix ave/time command","fix aveforce command","fix balance command","fix bond/break command","fix bond/create command","fix bond/swap command","fix box/relax command","fix colvars command","fix deform command","fix deposit command","fix drag command","fix drude command","fix drude/transform/direct command","fix dt/reset command","fix efield command","fix enforce2d command","fix evaporate command","fix external command","fix freeze command","fix gcmc command","fix gld command","fix gle command","fix gravity command","fix heat command","fix imd command","fix indent command","fix ipi command","fix langevin command","fix langevin/drude command","fix langevin/eff command","fix lb/fluid command","fix lb/momentum command","fix lb/pc command","fix lb/rigid/pc/sphere command","fix lb/viscous command","fix lineforce command","fix meso command","fix meso/stationary command","fix_modify command","fix momentum command","fix move command","fix msst command","fix neb command","fix nvt command","fix nvt/eff command","fix nph/asphere command","fix nph/body command","fix nph/sphere command","fix nphug command","fix npt/asphere command","fix npt/body command","fix npt/sphere command","fix nve command","fix nve/asphere command","fix nve/asphere/noforce command","fix nve/body command","fix nve/eff command","fix nve/limit command","fix nve/line command","fix nve/noforce command","fix nve/sphere command","fix nve/tri command","fix nvt/asphere command","fix nvt/body command","fix nvt/sllod command","fix nvt/sllod/eff command","fix nvt/sphere command","fix oneway command","fix orient/fcc command","fix phonon command","fix pimd command","fix planeforce command","fix poems","fix pour command","fix press/berendsen command","fix print command","fix property/atom command","fix qbmsst command","fix qeq/point command","fix qeq/comb command","fix qeq/reax command","fix qmmm command","fix qtb command","fix reax/bonds command","fix reax/c/species command","fix recenter command","fix restrain command","fix rigid command","fix saed/vtk command","fix setforce command","fix shake command","fix smd command","fix smd/adjust_dt command","fix smd/integrate_tlsph command","fix smd/integrate_ulsph command","fix smd/move_tri_surf command","fix smd/setvel command","<no title>","fix smd/wall_surface command","fix spring command","fix spring/rg command","fix spring/self command","fix srd command","fix store/force command","fix store/state command","fix temp/berendsen command","fix temp/csvr command","fix temp/rescale command","fix temp/rescale/eff command","fix tfmc command","fix thermal/conductivity command","fix ti/rs command","fix ti/spring command","fix tmd command","fix ttm command","fix tune/kspace command","fix vector command","fix viscosity command","fix viscous command","fix wall/lj93 command","fix wall/gran command","fix wall/piston command","fix wall/reflect command","fix wall/region command","fix wall/srd command","group command","group2ndx command","if command","improper_style class2 command","improper_coeff command","improper_style cossq command","improper_style cvff command","improper_style distance command","improper_style fourier command","improper_style harmonic command","improper_style hybrid command","improper_style none command","improper_style ring command","improper_style command","improper_style umbrella command","include command","info command","jump command","kspace_modify command","kspace_style command","label command","lattice command","log command","mass command","min_modify command","min_style command","minimize command","molecule command","neb command","neigh_modify command","neighbor command","newton command","next command","package command","pair_style adp command","pair_style airebo command","pair_style awpmd/cut command","pair_style beck command","pair_style body command","pair_style body/rounded/polygon command","pair_style bop command","pair_style born command","pair_style brownian command","pair_style buck command","pair_style buck/long/coul/long command","pair_style lj/charmm/coul/charmm command","pair_style lj/class2 command","pair_coeff command","pair_style colloid command","pair_style comb command","pair_style coul/cut command","pair_style coul/diel command","pair_style born/coul/long/cs command","pair_style lj/cut/dipole/cut command","pair_style dpd command","pair_style dsmc command","pair_style eam command","pair_style edip command","pair_style eff/cut command","pair_style eim command","pair_style gauss command","pair_style gayberne command","pair_style gran/hooke command","pair_style lj/gromacs command","pair_style hbond/dreiding/lj command","pair_style hybrid command","pair_style kim command","pair_style lcbop command","pair_style line/lj command","pair_style list command","pair_style lj/cut command","pair_style lj96/cut command","pair_style lj/cubic command","pair_style lj/expand command","pair_style lj/long/coul/long command","pair_style lj/sf command","pair_style lj/smooth command","pair_style lj/smooth/linear command","pair_style lj/cut/soft command","pair_style lubricate command","pair_style lubricateU command","pair_style lj/mdf command","pair_style meam command","pair_style meam/spline","pair_style meam/sw/spline","pair_style mgpt command","pair_style mie/cut command","pair_modify command","pair_style morse command","pair_style nb3b/harmonic command","pair_style nm/cut command","pair_style none command","pair_style peri/pmb command","pair_style polymorphic command","pair_style quip command","pair_style reax command","pair_style reax/c command","pair_style resquared command","pair_style lj/sdk command","pair_style smd/hertz command","pair_style smd/tlsph command","pair_style smd/tri_surface command","pair_style smd/ulsph command","pair_style smtbq command","pair_style snap command","pair_style soft command","pair_style sph/heatconduction command","pair_style sph/idealgas command","pair_style sph/lj command","pair_style sph/rhosum command","pair_style sph/taitwater command","pair_style sph/taitwater/morris command","pair_style srp command","pair_style command","pair_style sw command","pair_style table command","pair_style tersoff command","pair_style tersoff/mod command","pair_style tersoff/zbl command","pair_style thole command","pair_style tri/lj command","pair_style vashishta command","pair_write command","pair_style yukawa command","pair_style yukawa/colloid command","pair_style zbl command","partition command","prd command","print command","processors command","python command","quit command","read_data command","read_dump command","read_restart command","region command","replicate command","rerun command","reset_timestep command","restart command","run command","run_style command","set command","shell command","special_bonds command","suffix command","tad command","temper command","thermo command","thermo_modify command","thermo_style command","timer command","timestep command","<no title>","uncompute command","undump command","unfix command","units command","variable command","velocity command","write_data command","write_dump command","write_restart command"],titleterms:{"break":215,"default":[37,39,40,55,57,58,59,61,62,71,87,88,92,103,104,106,108,109,120,124,125,142,148,156,157,161,167,168,171,173,187,189,190,191,193,194,195,196,198,199,200,202,203,204,206,210,211,212,215,216,218,219,220,221,225,228,231,232,237,239,240,241,242,243,245,250,253,255,256,260,276,277,281,282,285,286,287,288,289,291,294,296,297,299,300,314,316,321,322,323,324,327,329,331,333,337,350,353,355,356,358,359,361,362,364,366,367,368,370,373,377,379,395,416,417,422,424,432,433,449,450,464,465,466,469,470,472,474,476,477,478,481,483,485,486,487,488,489,494,496,497,498],"function":495,"long":[208,378,380,381,382,383,387,389,390,407,411,415,427,435],"new":8,"static":12,acceler:1,ackland:64,acknowledg:7,adapt:[198,199],addforc:200,addit:[12,13],addtorqu:201,adiabat:6,adjust_dt:304,adp:371,airebo:372,alloi:393,amber2lmp:13,amber:6,angl:[8,65],angle_coeff:22,angle_styl:[2,20,21,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38],angmom:66,append:202,arrai:6,aspher:[6,82,146,257,261,265,266,274],atc:[9,203],atom:[6,7,8,64,67,70,71,72,73,76,77,78,80,81,85,92,96,97,100,101,102,108,112,113,115,142,143,166,202,204,205,288,495],atom_modifi:39,atom_styl:40,attract:5,aug:[],aveforc:213,awpmd:[9,373],balanc:[41,214],barostat:6,basal:67,beck:374,berendsen:[286,317],between:6,binary2txt:13,bodi:[6,8,42,68,147,258,262,267,275,375,376],bond:[8,13,69,215,216,217,295],bond_coeff:44,bond_styl:[2,43,45,46,47,48,49,50,51,52,53,54,55,56],bop:377,born:[378,389],boundari:[7,57],box:[6,58,218],brownian:379,buck:[380,381,389,418],bug:3,build:[9,11,12],calcul:6,call:12,categori:2,centro:70,ch2lmp:13,chain:13,change_box:59,charmm:[6,20,174,382,415],chunk:[6,66,71,75,90,94,105,107,116,148,163,165,206],citat:7,class2:[21,43,175,340,383],clear:60,cluster:72,cmm:9,cna:73,code:6,coeffici:6,colloid:[331,385,461],colvar:[9,13,219],com:[74,75,149],comb3:386,comb:[291,386],come:5,comm_modifi:61,comm_styl:62,comman:[],command:[2,6,8,12,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167,168,169,170,171,172,173,174,175,176,177,178,179,180,181,182,183,184,185,186,187,188,189,190,191,192,193,194,195,196,197,198,199,200,201,202,203,204,205,206,207,208,209,210,211,212,213,214,215,216,217,218,219,220,221,222,223,224,225,226,227,228,229,230,231,232,233,234,235,236,237,238,239,240,241,242,243,244,245,246,247,248,249,250,251,252,253,254,255,256,257,258,259,260,261,262,263,264,265,266,267,268,269,270,271,272,273,274,275,276,277,278,279,280,281,282,283,284,285,286,287,288,289,290,291,292,293,294,295,296,297,298,299,300,301,302,303,304,305,306,307,308,310,311,312,313,314,315,316,317,318,319,320,321,322,323,324,325,326,327,328,329,330,331,332,333,334,335,336,337,338,339,340,341,342,343,344,345,346,347,348,349,350,351,352,353,354,355,356,357,358,359,360,361,362,363,364,365,366,367,368,369,370,371,372,373,374,375,376,377,378,379,380,381,382,383,384,385,386,387,388,389,390,391,392,393,394,395,396,397,398,399,400,401,402,403,404,405,406,407,408,409,410,411,412,413,414,415,416,417,418,419,420,421,422,423,424,425,426,427,428,429,430,431,432,433,434,435,436,437,438,439,440,441,442,443,444,445,446,447,448,449,450,451,452,453,454,455,456,457,458,459,460,461,462,463,464,465,466,467,468,469,470,471,472,473,474,475,476,477,478,479,480,481,482,483,484,485,486,487,488,489,491,492,493,494,495,496,497,498,499],common:3,comparison:1,compos:6,compress:9,comput:[2,6,8,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167,495],compute_modifi:103,condit:7,conduct:[6,322],constant:6,constraint:7,contact:[76,122],contact_radiu:[],coord:77,core:6,correl:[207,208],cosin:[23,24,25,26,27,28,177],cossq:342,coul:[378,380,381,382,383,387,388,389,400,407,411,415,427,435],coupl:6,creat:216,create_atom:168,create_bond:169,create_box:170,createatom:13,creation:7,csld:318,csvr:318,cubic:409,cuda:[9,14,111,114,145,155,200,213,227,230,234,255,264,301,302,317,319,330,378,380,382,383,393,399,400,407,408,410,413,425,451,453],custom:8,cut:[49,373,380,383,387,390,395,397,407,408,415,423,427],cvff:343,damag:[78,123],data2xmovi:13,data:6,databas:13,deby:[387,407],dec:[],defgrad:129,deform:[151,152,220],delete_atom:171,delete_bond:172,delta:24,deposit:221,descript:[20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36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